-An option to play 1-on-1, 2-on-2 or 3-on-3 against the CPU in the Xbox 360's practice court.
-(More) custom moves for players. I'm not sure if I noticed any in 2006 (I think I saw LeBron's signature dunk as well as some Josh Smith exclusives), but some moves like Jason Kidd's off-the-glass alley-oop or Nash's sly dimes would be cool.
-Make the block button pressure-sensitive. I don't know if I'm alone, but I find myself jumping prematurely a lot during a game, because, unlike real life, you can't stop yourself once you hit the block button. But if it were pressure-sensitive, you could start to press it but stop yourself once you realize it's a pump fake or whatever, and your man will only lift his arms and maybe jump forward slightly, but won't commit fully to the block.
Also, if you pressed it with all your might, you'd be able to do a powerful block with the likes of Josh Smith, Ben Wallace, etc., which disallows an immediate second-chance opportunity for the offense, but increases the chance of a shooting foul.
If you tapped it with a normal amount of pressure, you'd do a lighter, less aggressive block, but you'd be less likely to foul.
-Allow the editing of Freestyle moves. I find that some centers have freestyle moves that may be useful for guards/forwards, but I can't allow them to do it without lowering their handling ratings (I believe). Editing freestyle moves would get rid of this problem.
-Allow for manual celebrations after a play. The upside? It can rile up a home crowd and hype up teammates, or silence a road audience and affect the status of your opponent, which gives you more momentum. The downside? You can be teched for excessive celebration or hanging on the rim.
-Allow for manual arguments of calls. If you actually have a case, maybe the referee will give you the call in the same situation later (when, if you hadn't confronted him, he wouldn't have). However, like the above, you are able to be called for a technical foul or even thrown from a game.
Also, star players should have more ability to sway the refs their way by confronting them than less notable players. It's all risk-reward. You can use your number one player to argue a call, but he may get ejected. The decision is there.
-When one calls a play, provide the player with a handy arrow or something of the sort to direct him as to where the ball should be at a given time. He doesn't have to follow the reminder, but it'd be handy to actually execute a play like they would in the NBA.
I hope people like these suggestions; I'll likely be adding many more as time goes on.