I can't see buffing citadel upgrades helping, a team full of poor players is unlikely to buy them anyway, not to mention they would have less money than the leading team to do so.
The only real solutions are integrated voice chat and auto-matchmaking. I don't know how likely either are. Steam has integrated voice chat, though generally once you join a game it's handeled by the server on which you play. Still though, there's one-to-one voice chat available directly through steam and I assume the impulse overlay could co-ordinate that if SD thought it were a worthy investment. If they did incorporate voice chat, I can guarantee you I would check mics on my team in every lobby and bail/kick if a pug didn't have one.
Team matchmaking, clan wars, etc. have been mentioned, but I've never seen a strong commitment to their timely release. I assume the majority of resources for this game are being put into fixing bugs and connectivity issues, but of course I don't really know what's going on behind the scenes.
As for actual game mechanics, a de-emphasis on items in general and base stats improvement, allowing gold collection from mines/cit upgrades while dead, etc. would make the game less puntive when bad players torpedo a team, but I'm not sure they would actually make things more fun.
For the most part you've just gotta be resigned to not just checking your team's stats pretty religiously if you're not in the mood for a headache, but also making sure you have talkers on your team before the game starts. If they're not willing to say "what's up" back to you in the lobby they're not likely to tell you when they're going to go home and shop, when they need you to teleport to save them or assist on a kill, etc.
So in the end I defer to the guy in this thread who said "give pantheon a try." This round is a bit unfair with the generals vs. assassins (fun if you're a general though), but generally it's a fun way to get a string of reasonable games going. Much less frustrating than lobby games in my experience, though your mileage may vary.