Framerate in SotC is a problem in some of the really big bosses - the last one is the worst for framerates and gameplay, so there's no reason to play it other than to see the amazing ending.
I submit that a game is more than the sum of its parts. I do not snub my nose at bad graphics or story, why should I therefore snub middling controls or framerates? If any of these elements are so terrible as to detract from the experience, then the game may be flawed. I don't believe that's true in SotC at all. The controls in SotC are beautifully difficult to master, turning the colossi into terrible mountains. (I've maintained for years that the bad controls in Resident Evil games prior to number 4 were brilliant, and RE4's new controls aren't that much better. Bad control is a part of the aesthetic.)
If I believed that every part of a game must be good, that is, when I played a game I honestly said "These graphics are good, the controls are good, the gameplay is good, the sound is good, ergo, this game is good" then I am not looking at the game at all. I have not asked why the game exists, what its purpose is, what I am supposed to gain from it. If I ask this I may find that the game is intended not to be simple but complicated, not fluid but scary. I may also see that the game's story and presentation are ten times more important than its length or depth. Tough pills for Nintendo fans to swallow, I know.
As for framerates, I don't know how anyone who ever played the N64 could ever criticize framerates and call them a deal-breaker. Banjo-Tooie (and sometimes Kazooie), Perfect Dark, Vigilante 8, Blast Corps, Turok 1 and 2, Winback, Body Harvest, Castlevania, Bad Fur Day, Jet Force Gemini, Pilotwings, Starfox 64, even the two Zelda games! Each one of these had framerate issues, some worse than others (Nintendo was pretty good at avoiding them, others were not). System limitations did not keep these games from being beautiful and compelling, even though they were at times very difficult to play. I propose that SotC has better framerates than any of the Rare games (minus Blast Corps) I have mentioned.