This is something that I've been thinking about for a little while now. I can't really seem to think of very many great (or even good) boss fights from FPSs (or, for that matter, TPSs, either). Might this be something inherent to the genre? I've been toying around with the idea that some of the things that tend to make FPSs "fun" (e.g. mowing down enemies, smart positioning, movement) don't mesh well with some of the more traditional boss fight tropes (e.g. lots of health, long battles, high damage/risk "attacks").
I also think that it's certainly possible to make great FPS boss fights, but those tend to be due to creative ideas that don't necessarily lend themselves well to repetition (e.g. set-piece moments/fights).
I just started thinking about this in relation to Borderlands 2, a game that I thought didn't have the most creative boss fights (in large part, they felt like enemies that just happened to have more health -- so you just shoot more bullets at them -- and that do more damage). [Note: this is not supposed to be a "hey let's all rag on Borderlands 2!" thread, that is merely a jumping off point. I like Borderlands 2 just fine!]