First off, I'm REALLY glad to see this project exists. I really hope to see it completed and be able to play X-COM on Win7 without DOSbox! Fortunately it runs fine on XP.
Anyway, I know you're probably getting bombarded with ideas (or will soon), but one thing that would be really fantastic if you removed all the stuff like the 80-item limit and the 40-units-per-side limit would be a way for users to create scenarios where they can specify how many aliens arrive in a terror mission or in a base assault, and the number of civilians in a terror site. This way, you could create absolutely mindblowingly crazy situations: a terror site with 50 civilians and 10 Chryssalids, a base assault with 200 Floaters and 30 Reapers defended by 40 guys and 60 tanks, whatever!
I don't really know how it could be implemented from a UI standpoint, but maybe some kind of save game editor would do the trick, allowing you to manually place objects in the battlescape from a save. This could also allow for mixed-race attacks, Ethereals and Floaters and Snakemen, etc. Something like that could be tons of fun to mess with, and I'm not sure if it's possible currently (without a lot of effort at least).
Good luck on this project!