The problem with boss battles is that most are not well done. Halo 2 for example how many times did johnson head shot that brute, plenty of times. But when you play regulary against enimies who aren't bosses they aren't exactly given the special privelage to absorb your bullets. Bosses become bullet sponges in most games espeicially FPS, or a QTE which is just bad. Another example is halo 4 , some people were dissapointed by the ending , but think about how that fight would go, you'd shoot him up after dodging an attack. Damaging him and then he jumps away and sicks enimies on you.
Too make a good boss battle you have to be able to put the boss on the same level as if you were fighting any other enemy. Even if the battle ends quickly because of how good the player is at the game. The boss also has to take visible damage, and show a desperation like sweating or becoming more aggressive. Theres also nothing wrong with calling in reinforcements but i believe the boss should call out to them. Come to his aid and swarm around him to protect him. The boss also has to be little bit more intelleligent than your average NPC, to make a good battle you need an intelligent a.i who can dodge and fight back as aggressive as the player. This isn't easy steps for an FPS.
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One thing I can't stick is bosses that change the rules or cheat, Tartarus is one good example. I'd also like to point at Vega/M bison in SF2 the amount of rage I use to have for him...