You're right, I was thinking about it in rather simplistic terms. There is no guarantee that chemistry will be built in keeping a poor group together, but on the other hand, if you are constantly buying and selling players you are not giving chemistry a chance at all. So, keeping players together would be a necessary if not sufficient condition.
Your point about inactivity also makes sense, that is certainly not ideal for an online game. Any chemistry factor would have to be rather complicated then. Personally though I just like the idea of my players 'growing as a team'. To me basketball is a game that feeds off of emotion a lot more than a sport like football. And strange things happen as a result. The Suns last season, for example. Or the Lakers' game 7 win over the Celtics. Intangible and irrational factors seem to play a significant role in the game, and I would love it if those factors were somehow brought into play. But implementing it and getting the balance right would obviously be tremendously difficult.
I like what some others have suggested about incorporating player personalities though - again, it might be tough to implement, but it would certainly add a lot to the game. Who knows, it might just be something we'd all enjoy if players appeared more humanized rather than a collection of bits.