Yeah, adjusting individual players' actual stats is a 100% non-no, in my book. However, something should be done to put the various "Eras" of the NBA on the same level. As it is now, 99% of players from the 50's and early 60's can't even be considered when the player pool includes everyone.
For example: If Wilt shot 55% efg, when the NBA average was 45% efg, and Shaq shot 55%efg when the NBA average was 50%, Wilt should shoot better than Shaq, to reflect that he was that much more above the NBA average. Same type system for rebounds and assists. Make dominant players dominant, no matter what "Era" they played. Think of an Open League where players like Cousy and Mikan would actually be usuable.
I don't know how to address this one, but I wish there was a "fear factor" in the Defensive ratings. As someone who watched a ton of NBA in the 80's, I shudder when I look at Laimbeer's ratings. Opponents were so afraid of what he (or Mahorn, or Rodman) would do if they drove to they hoop, that they did so much less than their normal, and when they did, it was with one eye "on the lookout" for what was coming.