The best experiences I've had playing cooperatively online have been in bf2142 and command&conquer generals. I haven't tried homeworld2, but I'll remember to check it out. Coming in fresh to this post and reading along, the best experiences of c&c online play came to mind most of all. Granted they were few and far between, and those of you who have also played there know it's not the game's problem ?
... but I was kind of hoping against the odds that 2-3 human players against the AI team would be fun in Sins of a Solar Empire too. I still kind of wonder if the element of betrayal, or "team-switching", is realistic or helpful. After all, there are many reasons why team members might want to consider their goal accomplished and move on after conquering their enemies. New game, new challenge, self-destruction not really a very smart strategy, etc.