Eh, the time thing ruined it for me too. I know you can slow down time, but that barely helps because the problem isn't that you don't have enough time, the problem is that you have a bunch of events occurring throughout time, and you can easily miss an event, or you end up having to wait for an event to start, then you get into repeatedly using the song of double time, the song that passes a day, the reverse song of time, and the song of time. I also hate having to schedule my time so as to make sure I'm doing the right quest on time, and that I'm never in the middle of a quest or in a dungeon when time runs out.
Plus it's a real piss off that you lose all "collectible" items like arrows and bombs when you reset time, because then you have to spend time collecting those before you set off again.
It also only has 4 main dungeons and is sadly short ignoring the side quests. (Yes I know the side quests are supposed to be the meat of the game, but I found most of them tedious)
Personally I think LTTP was the best Zelda, with OOT coming in close second. I don't find either of them any of the "greatest games of all time" though. They're good, great even, but not the best.