The Hitman series did boss fights up right for a shooter game. They were always normal enemies who could be killed exactly the same as other baddies, except they were often aware of you (so no stealth approach).
In Blood Money, for example, you meet another contract killer like yourself. He's also in disguise and challenges you to a battle to the death. You follow him into a warehouse to which he has the key. There are tables of guns laid out for you to grab. After a few seconds (enough time for you to load up), the lights go out. I should mention there are crates, boxes and those big metal racks they use in the back of the grocery store (in the employee-only area) all over the room. There's a maze of chain link fencing so you can't just run up to the guy and shoot him. He positions himself carefully, keeping cover between you and him. He doesn't have that much more health than an ordinary guy (chalk that up to Kevlar). It's realistic, tense and awesome.
But what's even MORE awesome is that Hitman doesn't betray its roots by forcing you into this fight. While it's true there are guards everywhere in this club (except said warehouse) you can STILL pull out a big freaking .357 Magnum and shoot this boss in the head, KILLING HIM WITHOUT ALL THIS NONSENSE if you want to. You just might also blow your Wanted level and ranking. But hey, at least you have the option.
Blood Money is one of the best games around. This is a small example of why. In fact, most of these Extra Punctuation complaint articles could probably be countered with "Hitman: Blood Money."