Personal favorite is Majora's mask, but I'm still saying OoT is the best well put together game of the series.
1, it was both kiddy and mature at the same time
2, It found a way to be completly serious, with very little "goofy characters/ bosses" there were bits of humour in the game, but they weren't done to clownish levels. I'm fine with a clownish/ jesterish character, but When the whole game goes that way it spoils it for me, like in ST/PH / (or the concept just makes you go, this is stupid like in ST)
3, It found a way to tell a good story, but kept it very basic
4, The cliche' of the game made it even better, it didn't feel like it was trying to pull some kind of gimic, it remained true to the Medieval knights kinda phantasy.
5, Time travel, who doesn't love time travel in their games? Now you could argue this was a gimic, it didn't feel like it was trying to be gimicy, but more as a transition.
6, Solid flow, combat didnt' feel clunky or hindered at all, and flowed smoothly, the story line progressed fairly well, you were free to explore or not, and could do most of the dungeons in various orders, and the story remained unchanged by it.
7, the lack of story telling in some parts, leads the player, or at least a player with an imagination to want to fill in extras
8, bosses were varried, and fun
9, dungeons were varried and fun (some improvements could have been done, master quest specifically spirit temple was breakable and uncompletable if you did it in wrong order) but as far as main OoT, can't really complain about the dungeons
10, The Ocarina was one of the best parts of the game, going around learning music, or just badly playing ocarina for fun, MM, did it great too, Seriously I know they don't wanna rip off OoT in that sense, but bring back a playable insturment, spirit tracks does have the flute thingy, and its one of the few things i can appreciate about ST so far, WW did it and granted it functioned the same, a wand is not to play.
There are places they game could have been improved, but it nailed all the groups I think.
Story 9/10 (personal 10/10)
Graphic 10/10 for the day, they ran smooth, and still look good to this day (notice i said good, not great) they were the right balance of colorfulness and gritty, depending on where in the game you were.
Gameplay 9/10 The game play was almost perfeclty smooth as well, seldom freezes, and bugs only really happened when you were trying to make them happen
GameFlow, 9/10 This one is hard to really describe, but has the biggest impact in how a game feels then anything, its part of how do you feel when you get to the next temple, are you too annoyed at something the blocked you getting here to care about the temple? Or are you excited to get in there? Do i feel like i was forced to come here? Or did I decide to come here? Am i free to go around and explore between temples, or do mini game? Or are all the damn bridges missing? Its ok to have an obstacle between objectives, infact it would be boring if there was nothing, but does this obstacle feel forced? Is it so stupid or annoying that I really don't feel interested/ motivated to finish it, and only do so in order to go on?
Best when these blocks can be motivated /disguised by the player investigating/ exploring. Like in OoT/ MM, I went Death Mountain and all the gorons are gone, well i'm a look around, find some skullulacha and try to throw a bomb at apperently the only goron left, oh hey the game goes on. TP- Go find light bugs and fight these screeching shadow things that have to die at the same time... But A double sword attack kills them in half the time then the doggy takes flying around, doesn't matter cause the dogy fly is apparently a single attack even if its taking 5 seconds, that makes no sense. Even worse when they just ambush you where ever you try to walk.
Windwaker, I loved the sailing, but when some stupid glider shark thing, won't leave me alone, its less love, Can't i just sail where i'm going in peace? I put 9/10 on OoT's flow because night as a kid, was frankly annoying, I wanna go where i'm going, and thats that. Dangerous things should only be in dangerous areas, not getting in my way going to the dangerous place.