1: one of those features that's really awesome for about 5 minutes until you realize how useless it is. I really can't see people taking the time to push boxes around when they can be attacking the enemy base or something. And as others have mentioned, it has too much potential for cheap tactics. If you can convince me otherwise, I'll consider it.
3: probably not hard -- I think lazarus has something like this, if you want to look into it and find the function names, I can copy it over easily.
4: hm, I'll have to look into it.
5: You can make custom flags, but they have to be .md2's. I think it's the "model" key in the flag ent.
6: yeah... that needs to be done at some point. It has something to do with thembeing drawn in a different order (they have to be drawn back to front). I just haven't gotten around to it.