I don't usually like it when they do that. That's one of the reasons I'm not a fan of boss battles in general.
A good example is the first boss battle in Deus Ex: Human Revolution. I'm playing the game with my character centered around stealth, which appears to be a primary option. Pretty much every situation, you can get through silently. Then, boom, by the way, forget all that because you have to beat this boss character in a straight fire-fight. Your character isn't built or equiped for that? Too bad. I was really, really pissed off about that.
On the other hand, you have Blood Dragon, which probably had the most beautiful and elegant ending for a video-game ever.








