I had the same problems with CPU shooting 70-80% 3-pointers against me, and 60-70% FG (I use Jared Hartung's tweaked rosters)
I just realized one thing: when you JUMP trying to contest CPU's shot, it seems to not reflect in the FG% (he will most likely make it with your hand in his face). Sure, you can block his shot, but I also got a lot of fouls trying to do so.
However, if you use the 'raise hands' action (I'm not sure how is it done in freestyle, but I play on keyboard and it is 'take charge' button when I press it without releasing near the CPU player who is shooting), CPU shooting percentage will be MUCH lower. I had a 16-12 season record on 4 minutes, superstar. But in the playoffs, after I started using 'raise hands', I won every single game - against Lakers, Kings and the rest by 10+ points.
Here how I play defense (I played for the Jazz): I set 'zone defense', and control SF (Kirilenko) on defense. I'm trying to position him near the ballhandler and press 'charge' button. 50% of the time I'm able to take good position and he will raise his hands when the CPU is shooting - and a lot of times CPU will miss.
This works especially great against 3-pointers. When it's the 4th quarter and CPU is behind, he starts shooting 3-pointers like crazy. It's quite easy to predict who will he shoot 3-pointer with, so I just raise hands while he's shooting, and his 3-pointer % is just about 10-15%, no matter how good his 3PT rating is.
The same things works great when defending against centers like Shaq - if he tries backing down, just take charge, and he will most likely be called for offensive foul. Even if he's shooting a very close shot, raising hands still can make him miss.
And this also never gives you a foul, which is very likely if you jump trying to block the shot.