I think both team-based and clan-based models have merit.
EVE: clan based.
POTBS / Battleground Europe / Planetside / DAOC / Warhammer: team based.
Team based has been the more popular model for developers but it's hard to ignore the fact that arguably the most successful PvP game of all time is EVE, and it's clan based. And EVE has some serious flaws, so I think it's telling that it has prospered for so long. I think part of it is that "clan loyalty" trumps "team loyalty". Long after the players of the team based games have stopped caring, the players of EVE still have clan loyalty and will sometimes come back just to fight for their clan again.
I'm in a small clan in Strategus. We have maybe 12 active players and we own one fief, which we gained and hope to hold with the help of allies (they show up for our battles; we show up for theirs). I feel this gives me more personal interest in Strategus than if I was simply in some broad faction.
What I think team-based setups do is help bring in solo players and very small groups. Since you are automatically in a team, you can contribute without directly needing to join a clan (or really be social at all). And there is merit to that. But I don't think it builds the long term personal connections that a clan based game can deliver. Clan based games force you to build social connections to survive and while that may turn away a lot of solo players, the players who DO build those connections tend to stick around.
Again, EVE is the shining example of this. Not to derail the conversation, but EVE ship combat is crap any way you slice it. The mechanics are just too simple and boring. But the game has been growing year after year because, I think, of the social connections it forces people to make. Once you're "in", you don't want to get out, and if you do get out, there's always someone you know still in that's tempting you to come back.
I think too many developers look to the short term benefits of team based gameplay and overlook the long term benefits of clan based gameplay.