I think that from technical side communication is totally enough, thus `.say()` and embassy suffice. Everything else, such as alliance mechanics, only restricts players (i.e. backstabbing).
Even if you don't have comms, you can gift tributes. If you have comms, you can also say "Please". How you'd think he will respond?
If you have comms, you can ask for other guys email or IM.
If you have comms, you can trade and share resources. We already have market system that streamlines it.
If you have comms, you can wage combined invasions. IMO you don't need cooperative enhancements, because coordination is the best you can have in the end anyway. And it is more fun to code coordination than to build "that cool super enhancement just because you happened to have ally". Also, together you also have higher surge (time to build X sized army close enough to enemy) than alone. Having military allies already is OP, lets don't make it even more.
If you have comms, you can wage combined invasions a lot further. Remember that GCL is exponential thus together you would have more controllable rooms than alone, thus you can have bases spread across wider regions.
If you have comms, you can agree to invade and seal a self-enclosing group of rooms together. Thus you would optimize your defense capacity A LOT.
If you have comms, you can agree to build wonders. For example decorative signs from walls. IMO super-power special wonders will only force players to play more cooperative just because it is more efficient. I'd prefer leaving it to players to decide how to play.
If you have comms, you can build mutual trust. IMO trust is more important than enforced alliance mechanics. Are you afraid of backstabbing? Well then you need to make sure that also a partner benefits from cooperation and he isn't a YOLO guy. But that's politics.
I am only saying that this is a cooperative game already with enough ways how to cooperate (after they introduced .say(), but even before that you could encode message in a "dance" with screep). But UX improvements would be nice. For example to have a blue color for myself, green and yellow custom lists of players and everyone else red. Also some metrics and highscores for "combined wars" or "mutual defences" would be awesome, even if non-official.