This is an age old problem in RTS's.
I'm one of those guys who don't play online with friends so I'm usually on the receiving end of this kind of problem.
The solution won't come in one big update but rather gradually over time.
One of the first things you'll likely see (ETA next couple weeks) will be that the connection info will put the player's experience score as part of their connection data.
This is one of the reasons why the stats not being robust right now is such a headache is because the skill rating stuff is ultimately useless without the stats being accurate. The stat handling being more robust should go up this week.
Now, from there, things get a little murky. I've made many journals on the issue with lots of different ideas. The tricky part is what can we do that won't split the MP community up?
Things like arranged teams and the like are great on paper but they do very little for casual players. I've been pushing for "random teams" for custom games. That's a bit more doable but I'm not sure how popular that feature would be either.
Skirmish and Pantheon provide a solution on paper but the problem there is that people simply quit before the game starts or just after the game starts if they don't get the combo they like which really ruins the game play experience.
In other words, there are no perfect solutions. My personal preference is randomized teams like I said.