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This is a dead horse topic - to even think about adding z-levels would require a near-entire re-write of the game.

Fiction primer says that there are not any true aliens in the main game, and there are numerous instances of Tynan confirming this in the forums.  If you want to ask someone to mod this in or make the mod yourself, by all means - do so.

Cold weather => people stay grouped in small areas with low air renewal.
People group in small areas with low air renewal=> Diseases.

Key points being "group" and "low air renewal".
Therefore the wrong assumption that cold = disease.

"How long influenza survives in airborne droplets seems to be influenced by the levels of humidity and UV radiation, with low humidity and a lack of sunlight in winter aiding its survival." - Journal of Infection
"Avian influenza viruses can survive indefinitely when frozen." - Center for Food Safety and Public Health, Iowa State University

There are a lot of factors that contribute to the delivery and propagation of infectious diseases, and cold/winter is one of those that has a significant impact on influenza.  Cold/winter is by no means the reason why someone comes down with the flu - that would be the virus - but it creates a lot of the conditions that lead to its spread, including confinement to closed quarters with other people.

I would be more interested in seeing some realistic means of introducing the strain of influenza to the colony (e.g., NPCs) and then simulating the spread of the disease within the shelter.  It would make more sense for 1-2 pawns to get sick and then need to make sure that they get bed rest, separated from the rest of the group, to ensure that those infected get better and don't get anyone else sick in the mean time.  If the player forces them to interact with the rest of the group (e.g., combat, work, getting their own food), then there should be greater risk of additional infections.

I would probably set a task on the zone to "Optimize", which would at least attempt to combine stacks within the zone.  Keep it as a Haul activity, so it would not take priority over skilled labor activities and such.  You could also have an "Always Optimize" toggle for the zone, where any placing of materials in the zone would force an optimization for that material only.

My general rule of thumb when it comes to gaming is $1 for every hour of gameplay; really good/sharp/innovative games are worth more. I've played Rimworld for hundreds of hours, possibly more than a thousand, so I've easily gotten my money's worth. I would easily pay for the cost of another game to further significant development on this one.
That said, I am much more interested in seeing what Tynan will do next. I have been impressed with his creative vision, his dedication, his willingness to implement ideas from the fanbase, etc. I would rather put my $30, $50, whatever, towards something new from Tynan than keeping him locked into making incremental improvements (especially if he seems unwilling to hand over the keys to his "baby").
We have a creative mod community that can expand this game in so many amazing ways. Let Tynan go so he can create another world just as cool as this. I'm looking forward to it.

Keep the automatic naming, just add in the rename function.

While I don't think you could pull off a true zero-atmosphere option for RimWorld without making it almost entirely another game, I think you could go with some different atmospheric qualities to make it more of a survival challenge.  There is already a pretty good example of how a problematic atmosphere could work in the game - Toxic Fallout.  However, the game does not currently have systems in place that allow colonists to still get outdoor work done in any appreciable fashion without taking serious damage.

I think your starting point has to be coming up with a way to show atmospheric quality and how it changes based on access to air sources.  This should work similarly to the temperature systems, with a room having an air quality value (or values) based on how much air mixes when doors open up from adjacent areas (or just through the walls/doors) and whatever objects are capable of changing air quality are in the room.  For example:  a room could be next to another interior room connected by a standard door, which would not necessarily have a good air barrier rating.  The room could also be connected to the outside with a tent airlock, which blocks nearly all air movement when a colonist walks through, but the process of moving through takes significantly longer than a more structured airlock and much longer than a standard (un)powered door.  (Airlocks would also likely have good ratings for controlling temperature change from area to area.)

Why would you need to be worried about atmospheric quality?  Like the Toxic Fallout above, alien microbes, pollen, or other particulates could be harmful over time when inhaled - these could be countered by filter masks and air scrubbers.  Or the atmosphere could be oxygen-thin, leading to decreased activity by colonists in those conditions - supplemental oxygen would be needed.  There could also be atmospheric conditions, either periodic (sandstorms) or consistent, that cause damage to objects exposed to them, including clothing and weapons/turrets - certain outfits (e.g., hazmat suits, tough leather dusters) would be more resistant to damage and protective of underlying layers, and maintenance of objects and items could be done.

How would you start the game if this is implemented?  Currently, the initial group of colonists comes to ground in lifepods that crack open after landing and are otherwise just scrap.  I would instead recommend having a lifeboat come down, basically a small room with an airlock and a few inoperative cryptosleep pods (which can be used as beds).  Any other supplies that come down with the lifeboat (e.g., steel, wood, food) would be scattered around as usual or tucked into a corner of the lifeboat cabin.  The colonists could use the lifeboat's systems until they run out of juice (it can be connected by conduit to an external power source to keep them going longer), or they can strip it for parts.  Once the colonists have their own shelter up, with air quality and temperature controls in place, they won't be anchored to the lifeboat in whatever precarious/unproductive location it might have arrived in.

How would your shelter look different from now?  Most obvious would be the inclusion of airlocks and air scrubbers.  Airlocks would be, in total, around 2x3 or 3x5 cells in size, placed across a shelter wall.  Smaller locks use simpler materials, but are slower to use, less effective as an air/temperature barrier, and more prone to damage and maintenance issues, while the larger locks are quicker, more efficient, and more robust, but more expensive to build.  Air scrubbers would likely look very much like the current air conditioners, with a similar good/bad air color scheme to the cold/hot colors used for AC.  There would also either be a crafting table specifically for filter masks and similar equipment or they would be integrated into other tables.  There would be additional classes of doors (or at least ratings on the existing doors) to allow for air-tight doors to be installed from section to section in the shelter, to keep a breach in one section from automatically tainting everywhere else.

Colonists would gain filter masks, which could either be integrated into other hat choices or kept separate (existing hats could have filter ratings as well).  Outer clothing would have a rating for resisting degradation and damage to the colonist (but may also decrease the min and max comfortable temperatures - fine in colder environments but hell in the summer).  Similar to parkas now, colonists would automatically seek out outer garments that can protect them from damage and would mask up when air quality is low.

What do I mean by maintenance?  Instead of just building objects outside and not worrying about them unless they're attacked (e.g., gunshot, explosion, fire, warg bites), time and exposure to conditions would have a negative effect on the hit points of objects.  Static objects (e.g., walls, sandbags, furniture, joy objects) would just take damage, while functional objects (e.g., turrets, AC units, solar panels) would lose effectiveness as more damage is done, become inoperative after perhaps 75% damage and scrap after 100%.  Colonists would repair them as usual with a couple of differences:  rather than running around any time a single 1% of damage is done, thresholds can be set for when to send out the maintenance crews, and objects that get repaired a lot lose some of their maximum hit points. 

I would also apply this to weapons and other wearable items, e.g., having a rifle that has lost a lot of hit points be able to have nearly all repaired, but it drops from Normal to Poor in quality.  Clothing could be handled similarly.  Outside objects that have too few hit points could be repaired all the time to keep them together, but should more appropriately be replaced - like a coat that gets patched too much.

A lot to digest, I know.  Please let me know if you have any questions.

I have refined the evil thought into this - modular crafting table system:

Basically, you would start with a manual activity table that's only 1x2 or 1x3, and then you build adjacent modules that decrease crafting time, increase quality, improve material efficiency, or possibly automate processes.  Set the initial table down and then select an additional panel to build.  Each panel would have one cell that is just the overlapping link to the original table and then one or two cells that show the added functions.  The pawn would build the original table as normal, but each additional panel would be built at a slower pace the first time it's built, with the rate based on the pawn's Construction, Crafting, and Research skills, as they "tinker" their way to building the new components.  Once the first example is built (or a kit is bought from a trader or recovered in the field), later examples would be built at regular Construction rates.

The game just needs more content to fill it out. I always wanted players to have lots of options at any given moment, which is why I haven't added more tech barriers or hard progression. There just wasn't enough content to progress through without getting really niggardly with every little bit of content and irritatingly slowing down player progression and contracting options.

Since I think we're getting to the point where players have enough options to satisfy, I'm planning on adding some more 'development steps" in the next few alphas so there's more of a sense of progression.

Currently the thought is that for Alpha 13 (not 12) there will be an "electronics" resource which is needed for complex technical devices. It'll be really hard to get early game, costly but accessible mid-game, and in the endgame you'll be able to manufacture it yourself.

That's the idea for now, at least.

I also want to rethink exactly what research means. I mean, if someone joins who knows how to build a geothermal plant, why do you need to research it? There are a lot of logical issues with research IMO.

I've actually been lurking on these boards for quite a while, but I had actually had a burst of activity when I first joined, including my first post which talked about having many of the more complex technological items require an example piece (even non-functional) in order to determine how to make new pieces.  It also used an abstract resource similar to Tynan's "electronics" resource called "parts".

I think the key to this whole gated access thing is that it may not be so much a question of understanding the technologies at work, but instead having the manufacturing capabilities to put that knowledge to use.  I would say that you would need to create variations on the crafting tables that allow for greater and greater precision and functionality, from hand tools to power tools to machine tools and beyond.  You shouldn't be able to start the game with the ability to create a 3D printer or a CNC machine, but those might be things that can be unlocked through research or some kind of "tinkering" activity on a proto-crafting table.

Ooh, evil thought - back when I've refined it some...

what are the doctor's health stats regarding eyesight and manipilation? ie if the doctors have cateracts or arm/hand injuries/damage then they ARE worse at doctoring than without the cateracts/injuries/damage

Couldn't tell you specifically stats (I'm sneaking this comment in at work), but my two doctors are in good shape. They've been able to top 90% chance of success before with regular medicine and neither one has been injured or infirmed since they joined the colony (one is an original survivor).
Also, this is regarding trying to heal other colonists, so I'm not sounding a false alarm when it's just permissions for prisoners. It almost seems like the colonist needs to have their permissions checked on, but it isn't an option.

I am having a problem where my doctors (13 & 12 skill) are fixing up minor wounds, either with herbal medicine or standard, and the display message pops up "poor quality, 0% chance of good quality". This was working perfectly well for the first 6-7 months of the colony, but now is not. No real harm caused, but very frustrating and a strong enough excuse to start over again (it doesn't take a lot for me, but still).

"Refinements and bugfixing on flood-fill for fog clearing and zone creation"

It's about time we had some refinements on this show. - HHH

A small annoyance I have - is that when a cooler is chilling a room to -1, and the "hot zone" is -20, it still uses power. Surely the cooler could just open a vent to the outside and use no power at all.

^ Your thermostat takes power even when at the right temp. It has to keep monitoring the temp to know when to switch on again.

Then have the cooler/heater have three settings: standby, low, & high

i just dont know if my pc thats a bit olds can handle the game

For a while there I was running this game on an archaic beast, a desktop that I bought in 2000 or 2001, that I have done little to optimize in the years since. I was able to keep it chugging along until Tynan added the world maps. That is about as far as I would think you could get away with. (I now use a 5-6 year old machine that works just fine.)

Ehhh... I don't trust this game's melee system yet. You never know when one of those squirrels might wake up feeling like it's in a monty python movie and fill your colonists health table with silly bites.

"That Boomrat is dynamite!"