I think it's the only bad mainline Zelda game and one of the worst first party Nintendo games from one of their historical franchises.
The structure is a clusterfuck. The sky overworld is completely devoid of interesting things to discover with the exception of the pumpkin inn that might as well have been a part of the main town. Speaking of towns Skyloft is the only village in the game, all the other races are just scattered around the surface which adds to the feeling of artificiality of the world. The surface itself comes off as a succession of amusement park activities instead of a coherent, believable whole. The three main areas are extremely unbalanced, with only the desert being remarkable and the other two ending up boring at best. The dungeons are overrated (the Sandship is the only standout) with Ancient Cistern being the clearest example of style over substance (mechanically worthless, simple puzzles get spoiled by reading signs). If that wasn't egregious enough, Fi is a horrible companion character that never shuts the fuck up, spoils puzzles solutions out of nowhere and has nothing of worth to contribute when you ask her for hints. The gameplay scenarios are subpar, with the tadtone collecting, robot escort mission or first dungeon backtracking fetchquest being particularly miserable. Items are uninteresting with the exception of the beetle, the Imprisoned is a terrible boss that outstays its welcome immediately yet has to be fougth thrice, the pacing is disastrous with the endgame feeling like a slog and of course the motion controls are gimmicky and turn both traversal and combat into a shallow nuisance.
The game does a few things right (Skyloft is one of the series best towns, the music is great, timeshift stones are a legitimately genius mechanic and the Mogmas are a very likable new race I'd like to see return in a future game) but overall it's a mess and a definitive proof they ran out of ideas for the AlttP/OoT template and that it was more than time to shake things up and rethink the formula.