Updater: I think having an additional program that automatically installs updates would be awesome. Having to reinstall/repair every update is a pain in the ass.

4 Teams: Adding maybe a Red and a Yellow team would be awesome. Not every game would have 4 teams, obviously. Some maps couldn't fit them all. I think the server host could decide if they want 2, 3, or 4 teams. Additionally, teams could form an alliance with other teams, by a voting system (similar to the votekick) that could be initiated by anyone. Teams that are allied could still kill each other, but would not receive points for the kill. Also, they would be able to see the other team's location on the map. Allied teams cannot capture each other's intel.

Permanent Team Choice: One thing I've noticed (and am guilty of) is player's switching teams mid-way through a game, either because the other side is winning, to grief, or to maybe make the intel more accessible to their original team. Once a player joins a game, they should be made to stick to their choice.

Team Player Cap: This one should be obvious, and I don't know why it isn't standard. No one enjoys 25 on 6 match-ups. Make the cap like 16 or something, for fairness sake.

Finally, I would like to be able to know who I'm shooting at on the other team. You could have their name pop up either in their team color or red for enemy, like if you were looking at a teammate.