It's this kind of mentality that I am talking about, really. There are definitely cases where playing objectively might get you a lot of medals, but that also pulls other factors in such as class and whether you're Biochem or not.
And, hell, since nobody else is coming up with a solution for this, here's one:
Increase all rewards for a quicker win to beat out the benefit of farming. That way the dominated side isn't alienated. I also like the idea of map-specific medals. I'm surprised those aren't in to begin with, but if done badly they would encourage fighting and arguments among the team: "OMG you stole my cap!" says the Vanguard to the Sage that pulled him off a cap.
As for your juvenile "get good" suggestion. Sure, I'll get right on that. In fact, if that is simply the issue for EVERYONE, how about EVERYONE gets good and... oh wait, that doesn't solve anything. Nice try though.