Boy I'd make a lot of changes, probably too many to list here, but to start I'd:
Have the power five conferences break free from the rest and form their own division/association. Serving the best interest of both big schools like Ohio St. and small schools like Colgate is impossible, they are too different, and its a big part of the reason why the NCAA looks so foolish. Let the schools that want to pay players and be more of a semi-pro league play only each other and play by their own rules, but then effectively enforce every rule.
Have centralized scheduling like the pro sports have. The separation of the power five conferences will also mean the elimination of mid-major games. Its silly to let schools come up with their own schedule. Have every schools schedule dictated by whoever the new ruling body is, and eliminate RPI/BCS and any other strength of schedule matrix that exists. Make every team play the same amount of home and road games, and don't overload the schedule or force teams to play two games in three days. Keep the product attractive by letting the players rest and the coaches teach and prepare their kids for the next game.
Increase scholarship limits so more kids who need time to develop can sign with the best coaches and accept red shirts.
Dont try to pretend that the kids are there to be scholars. Make Basketball a major. Have the classes be things like Weight lifting. Calisthenics. Film Study. Shooting. Dribbling. Etc.
Widen the lane.
Increase the no-charge semi circle to a larger size than the NBA has (which in itself is much larger than the current NCAA version).
Make flopping a technical, you should not have to trick the refs to get a call. Watch amateurs who can't walk and chew gum at the same time pay basketball and nobody ever falls, watch the most coordinated and skilled players in the world play basketball and somebody falls on every possession. It should not be like that. No need to force these guys to fall just to get a call. Make flopping a technical and you might get a few bad technicals at first, but eventually players won't chance it and will stop flopping at all, and the technical will barely ever be called, yet the flopping will be eliminated from the game.
Enforce offensive three seconds.
Make it so it takes 6 fouls to foul out.
Extend the three point line to NBA range.
Drop the shot clock to 30 seconds.
Here is one every SU fan will hate because it will spell the end of the 2-3 zone, but I think its good for basketball as a whole to make it so there is both an offensive three second and a defensive three second call. I hate watching defenders just camp out under the basket and hope to draw a charge, that should not be what basketball is about.