You're missing the biggest part of the addons folder!
With PhysFS, GAE loads whatever is in the addons folder along with everything in the default directory, giving preference to the addons. So, if you want to change something about a faction, you just include the modified files in an addon and it will use the rest of the regular directory with that one modification. So for example, if you wanted to add the Japanese faction to Magitech, you don't have to copy the whole Magitech directory into addons. You just put the Japanese faction into addons and it will be included automatically at run time. In fact, an addon can overrule anything in the main data directory, including not only factions, tilesets, and maps, but also the menu models, team color textures, and (I believe) language files and fonts.
So, the big thing isn't just the compression, but the ease of adding a faction, tech tree, tile set, or map pack. It's much easier to tell a player "put this file in your addons folder and that's all" than it is to say "copy X here, put Y there, extract Z..." The old and complicated way might not seem bad to those of us who are comfortable with the file structure and rummaging through the directories, but I think the average player doesn't want to deal with this. PhysFS also supports links in Linux, so I've actually got it linked to my working directory for Solunar, which is in my Dropbox folder.
For 7zip/zip support: I don't know why it is like this, but especially windows takes ages to load games already now without zipped folders. Is this getting more worse with zip support? In multiplayer I often sit there and wait more than a minute waiting for those windows guys loading their games. Beside of this its indeed a great thing and will give us the possibility of a lot more features too ;-D
I also wonder what memory and CPU overhead zip and 7-zip introduce.
I haven't noticed any significant difference in game speed or load time with Linux. Maybe it's different on Windows or something, but I have no way of knowing.
Ready-made packages (which would have to be produced somehow, probably by mod developers), would improve ease of use / rule out some human error, though.
Yes, it's actually quite easy. The modder just has to respect the particular file structure. The player can already "just drop it in" with Constellus, for example.
Regarding auto-repair, I'm between the chairs, can find valid arguments for both points of view. Making it an option which defaults to 'off' is surely not worse than no implementation - besides of the work involved in doing it.
In GAE, it can be disabled globally in the *.ini file, and can also be toggled on a per-unit basis.
I hardly see if a house has a nice or a not so nice stonewall, because its so small regarding it with the default zoom. But maybe I am wrong. In general I cannot imagine that it is very complicated to introduce this deature ( if you know a bit more about opengl than me ). The main work will be creating these bumb maps ....
In GAE's version of Magitech, the bump maps are used on the Castle and Mage Tower, and they do make a noticeable difference to me. Of course, I don't think anyone cares to put bump maps on Pigs.