I honestly think the 3 pt percentages need to stay where they are to maintain any semblance of balance in this game. As several others have pointed out, scoring across the board is definitely up in the new engine.
Jonathan Stewart on my Rochester team is scoring over 18 PPG so far on 62% shooting against primarily -2 and -3 defenses. Granted my strength of schedule is not the greatest, but neither is Stewart. He's a solid D3 player, but not elite. My other team is HPU in Tark.
My center there just won conference PoY in a conference with 10 human teams. Granted it was a down year for the Great Northwest (7th in conference RPI), but still... That guy with his 626 overall doesn't look like a D2 CPOY in a conference with 10 human coaches. My point is that even pumping up distro to decent post players doesn't seem to damage their ability to score VERY effectively. Sure, they aren't generating quite the points per possession that a 42% shooting SG has, but they are absorbing a lot more fouls and potentially generating other advantages for the team in that way. If guards shot much more poorly these games would turn into virtual brawls and we could pretty much revert to the rules before they instituted the 3 point line. I'm not old enough to argue whether the game was better then, but if we assume that we want the game to look something similar to what we see in college basketball today then we better not change one set of percentages without a commensurate adjustment to the other.