(Everything I'm about to say is just my best understanding. I am not a dev, but I do remember many of the goals the devs have talked about)
Just to ease some of your concerns, there is plans to revisit the UI. The UI library that they were using was, as you have noticed, clunky and buggy. Sadly, they started on AVWW before they had a chance to work on that.
Thankfully, they found/worked on a much better UI library that is actually pretty good, which they are now using for AVWW. Once AI war becomes the focus again, they said they hope to port it to the new UI library, which will give them many more options to improve the UI.
The game used to have a mini-map (EDIT: a conventional mini-map, not the pop-up one when T is pressed), but as Keith pointed out, it was left out during the port for performance reasons. However, with a better UI library, they might be able to bring it back again, or bring it in again and leave it optional, so computers that cannot handle it don't have to.
The "alt or other keys being held down when switching windows" is sadly a Unity bug. Actually its a combination of two bugs, when the program is set to continue running when it loses focus. (Needed, so, for example, a pop-up doesn't cause a network disconnect in multiplayer)
1. There is no way to tell whether the game currently has focus
2. The engine does not properly update "key held down states" when the game loses or gains focus
Unity is the engine that AI war (Tidalis and AVWW too) runs on. They can't fix it themselves, because Unity is closed source. And yes, they have brought these bugs to Unity's devs/support team multiple times, and nothing has come from it.
And no, they probably are not going to make their own engine. They tried that once, and it had even more limitations then Unity did, and they found that the work needed to maintain an engine AND a game was generally not worth this level of control. EDIT: Possibly they could switch to another engine, but that still gives a large number of headaches for questionable gains. (Maybe the new engine is even less stable than Unity is)
And no, having it ignore modifier keys (shift, ctrl, alt) when they are held for a long amount of time is not really an option, as there are legitimate reasons for leaving modifier keys (and keys in general) for long amounts of time.