I'm going to half cheat right off the bat and say I would eliminate automatic reviews. All replays are coach's challenge, in all sports, and you get unlimited, but for each one you get wrong, it costs you a timeout. No timeouts = no replays. For baseball, an incorrect challenge would either add or subtract an out.
So with that overriding change...
NCAA Football
1.) Ban snaps during the first 10 seconds of the playclock until the final 2 minutes. Hurry up and wait, just to prevent substitutions has hurt the game from a viewer standpoint more than anything. Even the fastest teams almost never snap the ball that quick, it just removes the threat that they could.
2.) Remove waivers...for players and coaches. You transfer, sit a year. You switch schools as a coach, you sit a year. Obvious caveat if you were fired.
NCAA Basketball
1.) Remove charges. Coaching clearly teaching to take charges has changed the spirit of the rule. You extend an arm, offensive foul. You move on a screen, offensive foul. You stand in the pain like a guy blocking a free kick instead of playing defense, no call. It's your choice to defend that way, but if the offensive player can still finish through it, good for him.
2.) Go to NCAA baseball draft eligibility rules.
NFL
1.) Get rid of illegal contact. There is already PI and defensive holding, that's enough. Passing has become too easy as it is, there is zero reason for this rule to exist.
2.) Not sure the exact mechanism, but QB salaries impact on the salary cap have made it so you either need a top 2-3 QB or a QB in his rookie contract to win it. The worst thing you can have is a good QB, not on a rookie contract. Stafford, Flacco, Dalton, Cousins? You are screwed, and that seems messed up. Even Brady has always taken less, which has somewhat negated the impact of his contract.
NBA
1.) Get rid of advancing the ball on a timeout. It makes a late shot, but non-buzzer beater, meh, because the other team is going to get a solid response.
2.) Remove max contracts. I like the fact that you can keep your own FAs if you are willing to pay the tax, prevents the amount of roster turnover of the NFL, but the max contract is what creates all these super teams. If every team can only offer guys the same amount, then of course they'd rather go play with some other great players. Let the Suns overpay for a guy if they want.
MLB
1.) Ban shifts. At least two infielders have to be on either side of second, and can't be any deeper than the back of the dirt. The lack of balls in play starts here. Shifts take away hard hit singles and doubles. So guys swing for nothing but home runs, and are content to strike out, so the lack of action is striking.
2.) Salary cap and salary floor. I was never as in favor of this, because I liked teams' ability to develop their own talent, but the recent trend towards guys being so good, so early, has sort of ruined it. Teams milk guys on peanuts, which was ok when they then got paid, but that isn't happening anymore, because you can find another young cheap guy to fill the role.
NHL
1.) Honestly, nothing
2.) Same. I wish I liked hockey more, because their free agent system is the best in sports, and I can't think of a single rule change