Based on a personal opinion of course:
- OoT had better music
- OoT had a more epic atmosphere; Especially back then, the game was incredibly graphic. TP relied on a dark vs light atmosphere, where OoT already caught it better in the shadow temple.
- OoT was more challenging overall. I can't ever remember dying in TP or even getting close to that. Getting killed in a game isn't a bad thing for a game. It reminds the player of the challenge and all. If its too easy, the game can't feel epic anyway. The bossfights were laughable, especially since you could auto lock any boss; Especially Ganondorf in TP was a let down. the puzzles were easy or standard (pushing blocks on ice for example).
- Graphically, OoT was a much bigger graphic improvement. I found anything shadow related animated rather bland and simple. (Black pixels, or black walls with purple lines in it)
- Standard enemies were a lot harder in OoT and formed a decent challenge unlike in TP. The only guys that formed some challenge where the guys with full armor and claymores and mostly because they came in small groups or because of the lay-out of the room.
- Fighting has been way too simple in TP for my taste. OoT had a lot more standard moves and you had to rely on your shield a lot more. TP introduces optional fighting moves of which only a few are used on more than on a few occasions. Blocking attacks with your shield has been made way too easy in my opinion in TP.
- I didn't like the wolf link. Fighting with it is bland and arbitrary (depending on whether Midna feels out like helping or not) and most of the puzzles are simply based on wolf senses (either the nose or digging).
- I liked the populations in Oot better. Gorons are pretty much the same, but the interaction with the zora's, Gerudo's and sheikah was better in OoT. Now that I mention it, I can't remember any sheikah or gerudo's in TP. The Ooccoo especially seemed like they were thrown in for gameplay benefits.
- The dungeons in OoT felt more epic. I loved the shadow temple, the water temple (mostly for the challenge) and the desert temple for example. Also loved the side dungeons like the jail in Gerudo town, the ice cave before the water temple and the well where you get the magnifying glass. I must say, I really liked the idea of a city in the sky however and the temple was a challenge as well.
- The N64 controller was perfect for such games. It also made games like Goldeneye, Mario64, Banjo Kazooie and Perfect Dark a success. Some buttons on the Wii controler are really user unfriendly, which leads to never using those options.
Nitpicking:
- I had the feeling i had more camera control in OoT.
- Some area designs really bug me in TP. Who for example builds a temple on top of some palace? Lake Hylia with the huge stone suspension bridge with no pilars and of course the lake directly bordering a vast desert, only reachable by canon.
- I prefered the ocarina over howling to a stone.
- The thing in TP where you must jump in wolf form with the help of Midna seems very arbitrary. Why can we jump some ledges and some obvious ones not?
- Ilia in TP is really one of the worst and blandest love interests I've seen in a game.