See, I never liked any of the bosses in the TMNT games. Sure they could be badass, but it seems the only tactic is to try and find the right place to stand in order to hit them but just about avoid their instant retaliation.
I can't really remember any decent X-Men Legends or Marvel: Ultimate Alliance bosses, although the one at the end of X-Men Legends was OK. I remember you actually had to employ a bit of thought rather than the usual 'pound on them until they die'. Having said that, the first boss in Marvel: Ultimate Alliance 2 was alright; just a matter of keeping back the hordes of enemies, avoiding missiles and attacking when you had the chance. I was pretty proud of myself for beating that on the hardest difficulty with no deaths (you only get two 'healing tokens' at a time now)