What do you mean, his story is nicely cleaned up? His story isn't over yet. Aqua still has her promise to fulfil, and the letter Sora got at the end of KH2 was about Ven. Wait, you haven't seen the secret ending, have you? Or read about the final episode of coded?
And, no, the story of BBS wouldn't work if it were just Terra and Aqua. In that case, Terra wouldn't have been motivated to kill Master Erauqs, for one. Kind of a big development for Terra. I don't think anything other than trying to protect one of his most important friends would have spurred him into doing that.
If it weren't for Ven, Aqua wouldn't have unlocked Castle Oblivion to put him in as he slept, either. Which, importance for CoM and KH2 aside, was pretty important for Aqua's character development. Fulfilling her duties as a Master.
Xion's plot was self-contained and quite irrelevant (so far) because she was retconned into an existing time period that didn't mention her at all. You can't compare her with Ven, whose story seems to be one of the threads leading up to KH3.