Personally, Ocarina of Time 3D (yes, specifically the 3DS one because it's just so much prettier and more vibrant than the original...Grezzo did an amazing upgrade) is my favorite Zelda of all right now, but SS and TP are #2 and #3 and are very closely matched.
I really enjoyed the motion controls of SS and I loved the beautiful graphics and rich colors. I absolutely LOVED the streamlined menus and the save-statues to save at specific points and not having to start back at the beginning of an area/dungeon. I like SS music and score a lot, though like others have said it feels more "movie-background-music" at times with some themes that aren't very memorable. That said, I loved the characterizations for Link and Zelda and how alive Skyloft and all of the characters felt. I also really enjoyed the "overworld" areas outside the dungeon where they felt like obstacle courses and offered a lot of gameplay/exploration considering their limited sizes. I really appreciated that those areas leading up to the dungeons felt "dense." The dungeons themselves were really good...a bit linear and streamlined at times compared to other games' dungeons but I didn't mind since the overworld areas were kind of like dungeons themselves. SS bosses...all were good to me (including Ghirahim)...but I HATED the Imprisoned and the fact that you had to fight him 3 times. SS has probably one of my favorite stories of all, being the origin and just the presentation of it.
TP, at the time I really LOVED the cutting-edge graphics and the fact that it was a more mature, spiritual-successor to Ocarina...though now I have to say it does look dated...and the colors are a bit TOO muted at times. I loved that the dungeons were the focus of TP and they really shine...HUGE, sprawling labyrinths easy to get lost in and which take a long time to progress through, even if they aren't particularly challenging ever in the enemy department. TP's bosses are legendary...MASSIVE beasts, each fight pretty unique...very cinematic climactic boss encounters...just a shame none of them do any real damage so they're too easy. TP wins in music just because the themes (old AND new) are so memorable. I hope they go back to memorable themes again for the next Zelda on Wii U. I've beaten TP on Gamecube AND Wii and though I do at times like the precision of button-inputs, I enjoyed the aiming in TP and especially the fishing. Seriously...pretty pathetic that to this day the best fishing simulation on Wii is a "minigame" inside a Zelda LAUNCH title. Nintendo missed the boat by not having MotionPlus fishing in SS. TP wins in the travel...Epona is a lot better than a nameless loftwing...and I found the flying in SS to be tedious. TP wins for having a proper overworld, even if a lot of it is empty, boring, and useless and connected by skinny "tunnels." I liked TP's story a lot, though not as much as SS, but Midna is a lot more likeable and more well-developed than Fi. I never did and still don't like the bug-hunts in TP. Wolf Link is cool though.
So yeah, I could go on and on with the likes/dislikes for each and it's really hard to compare them directly...but when I just think about the two games (both of which I've beaten twice)...SS just has a little bit of an edge, mostly I think just because of the beautiful presentation and the more whimsical feel that to me Zelda should always have.
Now I just have to see if Wind Waker HD can jump in and displace any of my top 3 Zelda games. I've played but never beaten WW so I'm looking forward to seeing how it goes with what I'm hoping is the DEFINITIVE version of the game. :D
Upcoming Games To Get
Definite: Kirby Star Allies (Switch), Mario Tennis Aces (Switch), Fire Emblem (Switch), Yoshi (Switch), Pokemon (Switch), Kingdom Hearts 3 (PS4), Monster Hunter World (PS4)
Considering: Fe (Switch), Donkey Kong Country Tropical Freeze (Switch), The World Ends With You (Switch), Ys VIII (Switch), Street Fighter V: Arcade Edition (PS4), Kingdom Hearts 2.8 Remix (PS4), The Last Guardian (PS4), Shadow of the Colossus HD (PS4), Anthem (PS4), Shenmue 3 (PS4), WiLD (PS4)







