WCG:
Most of this is old hat to me but then I've been playing with Aurora since the beginning.
One thing to remember is that Steve originally created the game to assist him in playing a 4X campaign. The fact that he makes it available to us and supports it here, makes me very happy.
1&2. I think that he's have to lose some functionality to do as you suggest. Some of the game details are on the opening screen because users might want to change those for the current campaign. One common rule that those of us who played Starfire use is no NPCs until X turns. You can easily do that by setting the NPC chance to 0 when you start and then, later, opening the game and giving a non-zero percentage. The same goes for Berserkers.
3. I think it is because that file can be different for different versions of Windows. Having install instructions that tell you how to find and copy it would be nice though. If Steve wants to get really ambitious, he can have the install routine look where the file is suppose to exist and copy it automagically. Personally, I'd rather he spent his time getting 5.0 out the door.
4. The game is database driven. In the sense that you are talking about, the game continuously saves since everything is stored in the data base. Any time you exit and then come back, you will find the game in the state that you left it. If you want to save the game in case of crashes or the like, you can copy the .mdb file to another folder.
Welcome to the gang.