Agreed, really. I find a lot of boss fights boil down to one of two strategies: hit the boss with everything you have (RPGs, FPSs, action games in general), or waiting for/making the giant "fuck me" light to appear and hit THAT with everything you have (Zelda is one of the biggest offenders I can think of for this one).
And yet, it's pretty easy to think of some truly awesome and/or creative boss battles from recent games.
Starcraft 2. The closest thing to a "boss fight" in that game would be the last few missions of the campaign, and ye flipping gods, those are some epic missions. Speaking purely from the standpoint of boss fights being like final exams, the final mission is just that. Even on normal mode, it tests all your skills that you've (hopefully) honed through the course of the game. I found my heart was thumping in ways I hadn't felt in a very long while, and when I succeeded, it felt like a genuine accomplishment.
World of Warcraft. Anyone who plays the game will tell you that the boss fights, especially the raids, are no joke. Until you start overgearing the regular stuff. Then the boss fights become tedious or a fun romp, depending on your attitude. Personally, I tend towards the "fun romp" mentality, and even make it a challenge to see how fast I can nuke a boss.
Mario & Luigi: Bowser's Inside Story. Even when you learn when to press A to not die, it doesn't take very much for your rhythm to become completely messed up, making you concentrate and curse when you get hit even once.
Pokemon. Yes, sometimes it's a matter of luck. I don't care. It's Pokemon, and there's always at least a couple battles in every generation that will have you cursing the great cosmic forces. And then you have to try to catch the legendaries, no small feat.