Oh, here's a different direction: Kingdom Hearts: Birth By Sleep has an endgame that isn't bad, but it is fundamentally broken in a way you wouldn't expect. The fact that this problem occurs during the endgame is more of a coincidence than anything but I"m going to complain all the same. See: the game has you beat three storylines in three separate save files, and if you beat them with some particular hidden-but-easy-to-find items, it generates a fourth save file that you load and carries you on to the end game. Cute. Few problems:

Firstly, the finale file locks you out of an entire zone, the world where the finale itself takes place. This is bad if you're trying to unlock the true ending on Normal because you need 100% completion. The game doesn't warn you it's going to be doing this stunt (and certainly not of its flaws), so you have no choice but to go back to your old file, clear it and create a new fourth file, overwriting any progress you may have foolishly made in the old, nevermind that that's a complete rigmarole. Furthermore, progress in the fourth file just sort of lingers separately, leaving you two near-clones of the same character for multiplayer purposes, which is an even bigger deal in the Japanese expanded release as it has extra sections in the fourth file! (Unless the expanded release creates a fifth file, yeesh. I wouldn't know.)

There are hints throughout the game that there was originally only going to be one file and they changed gears, but this was not the right gear to change.

I have to insert Oblivion in that list : the shortness of the main quest comes as a gift when measured against the quality of its ending.

Trine.

Three of us played it together and only one of us was any good at conventional platformers, but that was okay throughout most of the game because it was most of a puzzle-solving experience instead of a twitchy button-mash.

...until you get to the last section, where the developers apparently just HAD to turn it into a twitchy button-mashing platforming thing. It ended up with the one good-at-platformers player finishing it later (after we'd collectively tossed the game aside to do something else for the rest of the get-together).

We never even bothered to look at the second one after that.

The flaw is the deliberate inconsistency in the game's design that obscures what strategy you're expected to use. As http://tvtropes.org/pmwiki/pmwiki.php/VideoGame/Terranigma?from=Main.Terranigma puts it:

Hah! I do believe I wrote that! It's worth saying that my stance has changed a bit since I did. I still think it's a good thing they encouraged the use of rings (though they probably should have done so in other places, at all, ever), but the trouble is that the Elec Ring, the only one that works in that case, makes you invincible while you use it. Sure, it encourages you to use all the mechanics, but it also turns things into a non-fight if you've bought enough rings, and if you haven't, you lose. Press X to win! Some middle ground would have been ideal - but that's a problem with the magic system, not the boss.