I would make every game with a LCD display have the screen be under the playfield like in Full Throttle and Alien, so I don't have to look up.

Small changes:
Give Addams Family more of an incentive to shoot combos and multipliers.
Give Star Wars Episode 1 an autolauncher
Some sort of optional setting on No Fear so that Infinite Loops stop being a viable tournament strategy.
Change Banzai Run to a theme that has more to do with the vertical nature of the game.
I haven't looked into it, but it is my understanding that the board game on safe cracker is not that strategically interesting. I would see about changing that.
Try to give the Beatles a different tournament strategy other than side-loops all day.
Starting a Magneto multiball on X-men without setting it up first and being punished with infinitesmal jackpots is kinda unfriendly game design. I understand that it's supposed to incentivize players to play in a certain way, but I would try to think of a different way to do that.
I don't remember exactly but I think in Whitewater there were certain parts of the game that never got shot for. The bumpers add chaos to the ball movement, but it would be nice if they did something more than that.
Left orbit on Theatre of Magic, the thing everyone complains about.
Wizard Mode on TOTAN being farmable. I don't know if there's a fan-mod that fixes this for tournaments.