OOT was the first RPG I ever played, so too much nostalgia here to be objective. That said, I liked TP more than OOT. For one thing, the storyline was constantly advancing in TP whereas in OOT it always struck me as annoying that they sent you after 5 talismans and virtually nothing of interest happened between getting that task and completing it in terms of plot development in what has to be 5 hours of gameplay. (probably closer to 8 if you did the water temple without a guide) I mean sure the sages were revealed but hands up anyone who didn't guess who the first three were anyway?
I was also pleased that they moved some of the action out of the dungeons in TP. In OOT the Gerudo Valley (crowning music of awesome right there, full credit to them for that) was virtually the only location outside a dungeon where there was any real adventuring to do. That said, I felt they skimped a bit in TP on the castle town; not enough minigames or people you could talk to. As for the last of the twilight bugs... well... least said about that the better I think. Also the spinner, very cool but it felt like something out of a sonic game. The dual clawshots on the other hand; pure awesome.
One thing that really stands out to me in favour of TP is atmosphere. They managed to stick together some scenes that were really touching or terrifying depending on what they were going for. (YOU NOT TAKE MIRROR!!! anyone?) Similarly the development of the characters was impressive; I mean we knew that the plot was going to get hi-jacked by Ganon before long (Ocarina of Time conveniently comes from an era before we got bored of seeing the same guy as a final boss over and over again) but Zant was still an interesting character to take the part of his lackey even if his animations were a bit hyperbolic. Majora's Mask deserves an honourable mention at this point as the one game in full 3D where Ganondorf doesn't even get a foot in the door.
On the topic of Majora's Mask I'm surprised that it's drawn so little attention. True it's not cut from the same cloth as the rest of the series so therefore the 'Legend of Zelda' title might've misled some people, but the repeatable bosses really make it one of the best games of all time for me. That said I'm a Monster Hunter fan, so that's probably why it appeals to me.
Soundtrack wise OOT has to hold the award though, it cannot be denied that the music was incredible. The closest TP comes is when it remixes OOT stuff so it can't really be given credit.
Either way, I think making a better game can be done; it just needs to be set in a desert. Wide open spaces, a new take on Hyrule and, most importantly, no excuse for a dungeon themed on water. Looking forward to Skyward Sword!