StingingVelvet: Half-Life 2 was an epic example.
And honestly timppu your puzzle boss ending is exactly the kind of thing that pisses me off. I just played a straight-up shooter for eight hours, I'm ready to move on and play something else, and here's this multi-phase puzzle ending. Fuck that shit.
Maybe I misunderstood you. I wasn't sure what was your original complaint, e.g. the end fights that are 10x harder than anything before, ie. making finishing the game very hard, just due to the end fight? I hate those kind of boss fights too, like the ones in XIII. The "puzzle" fights are usually quite easy, albeit potentially time consuming. Like e.g. the pit monster in Half-life (yeah it was not the end boss, but still, I feel it could have been a good one). Once you understand what you are supposed to do, it isn't that hard to achieve it.
Just today I finished GTA: Vice City. Its last story mission ("Keep your friends close...") wasn't hard at all, and also didn't deviate from the rest of the game in gameplay. So is that the kind of ending you prefer? I OTOH found that last mission kind of a letdown. Too simple, too easy, too anything but a memorable ending to a decent game. I just stood there at one spot shooting anything that moved for a minute or two, and poof, end of the game.
Of course, if I am playing e.g. a tactical game, I don't wish the end boss fight to be e.g. a pure action sequence, because I didn't want to play an action game. That used to be quite common complaint with many classic point&click adventure games, when they quite often had some simple but forced arcade action sequence, while rest of the game was pure adventure gaming. I can understand that complaint.