Don't forget that the perfect TDM trophy pretty much encourages base rapes (for those that care about trophies anyways) as it's the only way for a lot of people to get that trophy.
As for clan stacking, I've been in games where the game's inability to break up a clan meant my team was outnumbered 2 to 1. And the worst thing was that when new, non clan-members, players joined the game they were put on the opposite team. Naturally, when that happens people massively quit the server thus aggravating the situation. Can't blame them though, I do the same when my base is completely barren and 3 Hawks simultaneously cluster bomb me the moment I exit my drop pod.
Also, setting too high limits for matches, especially TDM, really doesn't help with the situation, a 30 min, 75+ points for a victory in a TDM will most likely turn into a base rape.
To help the other team when my team is base raping them, I'll usually try to give them a bunker and a shield. If they're not noobs or if they're smart they'll use them instead of destroying them.
We need either a surrender option that literally all the team (or 90%) agrees on, or capturable bases.
That would be cool for the times when people just wont go for the last objective.