There are a lot of changes I'd like to see. Putting aside judging issues (there are better systems you could have, but they're only better if you have competent judge and we don't), I'd like to see knees to the head of a grounded opponent, soccer kicks, and stomps permitted. Also the 12-6 elbow ban should be canned.
Another thing is that I don't think referees should be standing fighters up or breaking up the clinch nearly as much as they do, so they should either be prohibited from doing so at all or properly trained to do so only in the extremely rare case of a true stalemate that would go on essentially indefinitely. Oh, and Vaseline shouldn't be allowed on the face; it seriously interferes with grappling.
Another obvious one is giving guys time to recover from eye pokes. I can't believe they haven't done that yet. I'm also not a fan of the rarely noticed rule that says it doesn't count as an eye poke if it was a closed fisted punch. It seems to me to be a distinction without a difference. Also they should be stricter about enforcing certain rules--as it stands right now, you'd be a fool not to kick your opponent in the balls a few times and poke him in the eye, because the chances of getting a point deduction are miniscule. Same thing for grabbing the cage. I'd be interested in trying point deductions for blatant stalling as well, but don't have much confidence in the ability of our current crop of refs to really implement that well.
I'd like to experiment with longer rounds, too. I liked the 10 minute round in Pride but don't really think we want to get into a situation where rounds have different lengths again. Oh, and I think changing the shape of the cage would be good too. Round or octagonal cages let guys just circle away endlessly on the feet. Even if you cut an angle, you can't really corner them, they just have to adjust and keep moving away. Maybe the Octagon would still work if four of the sides were significantly shorter, so they kind of formed corners. But as it is now, it often rewards passive/"evasive" approaches to the stand-up game.
I'm sure I'm missing some things but that's what comes to mind right now. None of this is to say the current rules are all that bad. I'm still watching, after all. But I think we could do a lot better.