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I don't know why, but FPS games these days barely have any boss battles at all. Even the "final boss" in some games go down just like any goon. I think Serious Sam, Crysis, and Turok (the recent one) are the only FPS out there right now that has bosses that almost put up a fight. Serious Sam ends every level with a boss. I know you guys mentioned bosses, but please have more than 1 or 2 occasional bosses (see Crysis). Use Contra or Sin & Punishment as an inspiration instead.
Boss battles are old school. Although I prefer extremely intense fire fights against other "soldiers" or elite special ops over ridiculously powerful boss battles, they do still have their place when done right.