I once heard someone say that if OoT and MM were movies, OoT would be a summer blockbuster, while MM would be one of those small films you may not have heard of until the Oscars came around. Both are great, but they accomplish different things.
OoT had a more classic, grand, and epic feel to it, while MM was more emotional, intellectual, and artistic. Honestly, I think both compliment each other beautifully. OoT clearly set-up MM, and MM did what OoT didn't or simply couldn't.
I just can't compare the two and say one is better than the other- I have mad respect for both.