SS is OK to mediocre. Not great, not terrible. Has some clever and epic moments, has really dull sequences. Motion controls were OK aside from swimming and sometimes the bird view would freak out for some reason. But there's plenty to gripe about besides controls.
I can't see myself replaying it for awhile just due to the tedious travel time and retracing of steps. Seriously, you go up and down that volcano like 5-6 times. No one can defend padding like the tadpoles or using that dumb robot to carry things everywhere. Not being able to teleport between statues in a region is really frustrating. Before the last boss I saved, checked the time, went to Skyloft, refilled the potions, flew back, went back in time, saved before the last boss, and that took over 10 minutes. My final first time completion was about 35 hours but it felt like it should've really been a 15-20 hour game. If this was on the N64 I'd say it was because of cartridge limitations.
General negative points I noticed:
Here's an argument without end: which has a worse, more player hating overworld, this or WW? SS's is smaller but in WW you can eventually unlock instant teleports.
SS has very low enemy variety. 90% of the time you're fighting some form of bokoblin, keese, or chuchu jelly. Even in the very last dungeons of the entire game. There are no Like Likes, Wizzrobes, Iron Knuckles, Poes, Dodongos, Tektites, Bubbles, Wallmasters, Moldorms, Helmasaurs...and many others. Not that they had to copy-paste, just examples of what they left out from Zelda's now huge bestiary. The only cool new enemy I remember were the electric snails and the 3-headed hydras. But there's like 3 of the latter in the entire game. I guess they couldn't think of other sword direction gimmicks.
The music is probably the weakest of any Zelda game I've ever played. The only memorable ones were remixes. And the best remixes, like in TP, weren't even used (inexplicably) until the credits. There were some good boss ones with ominous Latin chanting and the little ditty when charging against the horde rush at the end. The main theme used in trailers is good but where was it in the game? Nothing from the main zones were memorable for me.
Two fire temples, really? And in the last one the big item lets you dig into 2D mazes and fight those dumb worm enemies like 10 times. No thanks.
Rolling bombs will give you early onset arthritis.
Everything after the third dungeon until the fourth killed the plot momentum.
Link's hat STILL clips through his shield.
Post Ocarina, in general, 3D Zelda dungeons seem to be getting worse. In TP and SS you pretty much always have 1 key at a time. Heck, there's barely ever more than one key in the entire dungeon. It feels very linear. And the rooms just aren't that interesting in many instances. When I think of OoT I think of that giant room filled with blades and invisible moving platforms from the Shadow Temple or the Spirit Temple filled with beamos and spiketraps or falling 1000 feet in the Fire Temple. Gone are little mechanics or action rooms like collecting silver rupees while avoiding obstacles or activating a timed switch and rarely are rooms full of enemies to kill. Plus in OoT and WW you can have a lot of different items mapped to buttons at once. In TP and SS it's one at a time, which really kills how complicated environmental interactions can be. It's just enter room, use item on environmental doodaad Y, open door.
This is a minor one, but I hated Link's ragged breathing and gasping after running 10 feet. If you were in the next room it'd sound like I was watching a porno.
Fighting The Imprisoned 3x...and the last two were very close to each other if you chose the forest first (like I did).
Pluses:
Often times optional, but better NPC arcs than most Zeldas.
The first dungeon's aesthetics: glowing mushrooms, white grass, spiderwebs everywhere, the blueish fog. And then you get the beetle.
Everything with the robot captain on the way to and including the pirate ship.
Anything with time crystals put a smile on my face what with seeing the world transform into its former glory. The sand ocean was trippy.
The trials changed up the gameplay and made you feel helpless. I particularly enjoyed seeing the starting town area sucked into this alternate dimension.
The fourth dungeon with the harsh demarcation of a happy, serene golden Buddhist temple with gentle flowing water vs. the purple Hades basement filled with zombies.
The action packed sequence leading to the desert dragon.
You could make the case that Ghirahim spent 90% of his time complaining about his own incompetence and he stole what could be real boss battles, but he was certainly interesting and not your generic bad guy. I loved his hammy lines and overdramatic gestures.
Last couple boss fights/areas were intense (ZERG RUSH!)
I feel like you could trace the noobification of gaming just by looking at Zelda starting areas.
LoZ: Has the attitude of "die in a fire player!" Bomb these walls that look the same as any other wall. Good luck making sense of these maze like dungeons where everything looks the same.
ALttP: 60 seconds in and you're killing enemies and collecting treasure. Signs and your dying Uncle provide control tips.
OoT: Does a good job considering it was one of the first 3D dungeon crawling action-adventure games. The first town explains new mechanics like z-targeting or all the various sword/dodging maneuvers and it only takes like 10 minutes. And if you want you can just skip that stuff, grab your junk, and head to the first area. The entire game suffers from inexcusable text crawl speed though.
WW: Similar to OoT. Your sis is kidnapped pretty soon. You have to learn moves from the dojo guy though.
Twilight: The beginning is bogged down by tons of required tutorials, mini-games, and sidequests. "GOAT IN!" two times, really? Just because this teaches you how to randomly kill the boss 30 hours later? Ugh, sooo slow. Just thinking about TP's start makes me not want to touch it again.
SS: Many required cinemas, tutorials on everything, Fi literally halts all gameplay to tell you very simple things from beginning to end (Navi always got a lot of flack but she only did that in the Deku tree; after that she barely talked for the rest of the game). It's a solid two hours of blather before your first dungeon.