will future releases allow for ingame patching/updating? I.E. I won't have to uninstall version 0.2xx and then download and install v0.2xx, because it'll update files and stuff ingame via online connection.

Currently, you only have to download a new version and install over top of the old copy. There's no need to delete the old copy, as usually the only changes are in the exe and some content files.
It's very unlikely that there will be an in-game patching system, because there isn't really much need in this case. Updates are generally released not as patches but rather as full versions, so it's easier to just download a new installer.

Plus the average rate of updates makes a patching program utterly unnecessary.

This might cause some problems though, if there's any more .rte changes, like when everything was split out of Base.rte.

Safest to do a clean install to a new location and copy everything you want over.

Ugh. Worst change ever in my opinion. I also miss being able to load up all the gibs (and place them in the scene editor if I so desired) from anything. The biggest problem now is if I wish to disable a faction entirely (Coalition or w/e), then I break any mods that reference effects or shots from that rte.

I think next build really should consolidate all effects/gibs/shots/etc back into Base.rte, and only split sprites and actor.ini files into separate factions.

What would be really nice is being able to make faction separations not by .rte but in the code itself, so that you could have more than one faction header in the same .rte.

Actually, wasn't there a whole string of suggestions at one time about how to manage the buy menu? Some of those, like collapsible faction and subcategories, would be really useful.

Oh collapsible faction options would ease the quickly bloated-by-mods buy menu SO much. I hate scrolling down to my custom content actors and then having to re-scroll on the weapons page to get to mod weapons each time!

Another suggestion is having a quantity option to quickly duplicate items in existing orders.

On a similar note, DFesque tags would be good for biological weapons and emps and all that.