I've not played most of the games mentioned here, but I do think a distinction should be drawn between boss fights that are hard simply because the difficulty level is insane and boss fights that are hard because they are badly designed. Now people may disagree about any individual case - about difficulty versus design of a particular endgame boss fight - but I think it is fair to say that some boss fights in some games are simply not well designed and are difficult because of that poor design rather than out-and-out difficulty. If one can back up with rational reasons that a particular end-game boss fight is hard because of bad design, then it is a fair post to make even if not everyone agrees. It's also the case that poor design may make the boss fight easier than the rest of the game or simply so substantially different from the rest of the game's gameplay (and may be easier or harder because of that) that one has to question the boss fight from a design perspective.
I totally agree with you, the fact is that I don't think multi-stage boss fights are a design flaw (unless, of course, it's a 10 stage boss fight, like the OP mentioned, that would be just ludicrous, unless there was something else to it). I had to grind my way through the Bloody Mary boss, on Terranigma (not even the end boss, mind you), but does that make the boss flawed? Sure, she was hard, but was pretty well designed, otherwise; it is possible to beat her, you just memorize her somewhat randomized patterns of attack and make sure you take a LOT of healing potions/rings with you, and then you prepare for a half-hour fight. When you beat her, the sense of fulfillment and accomplishment couldn't be greater. Obviously, when the game doesn't give you the tools and the chances to beat a certain boss, that's just plain poor design, and should count as the developer's fault, not the player's.