I've thought of a few things that would be nice to be able to do in MA/MAN, and am posting them in the hopes that they spark the devs' imaginations, even if they aren't implemented. For the moment, I'll stick with non-game stuff.
In-Game:
1) Background cutscene.
The cutscene that plays continuously in the background is really cool, but my computer just can't handle the stress of a dozen units firing and dying all at the same time. Thus, my sound tends to start skipping, especially when something tries to load (such as the challenge screen). It would be nice to be able to turn the cutscene off. At the very least, I would like an option to have sound disabled while out in the menus and enabled while playing without having to go through the options menu at the start and end of every turn.
2) Double challenge.
Right now, you can send/post challenges as PL, FNU, or Random. It would be nice to be able to send challenges as Both, where accepting a challenge as Both starts up two games with opposite side assignments.
www.massiveassaultnetwork.com (logged-in areas):
1) Stats.
It'd be helpful to be able to see other players' stats from the website, though I don't know how feasable this would be.
2) Challenges.
It'd also be handy to be able to send challenges over the website.
3) Chat.
Probably the least likely to be at all possible, being able to chat with the people who are online would be neat, though unimportant enough to be barely worth mentioning.
I hope this gives you Devs some ideas!