The Batman games are probably the best action-adventure hero games and certainly the best looking out there but I still have a soft-spot for Marvel Ultimate Alliance as a hero game.
As someone that was a casual comic-book fan it was first and foremost a fun game. However it was a brilliant gateway into the whole of the Marvel Universe introducing the more niche characters, locations, history and discovering the hero teams by mixing and matching teams. Just wandering around and speaking to Vision taught me so much about the backstories and bigger story-arcs to that time that it felt like I getting an encyclopaedia as well as a game. The whole thing felt like a passion project and not a quickly knocked out game.
Arkham City also deserves a lot of praise for letting you have all the equipment at once and not coming up with some bull to knock you back to a single bit of equipment. For the first game that trope made sense, but doing it with the 2nd would have cheapened it.
Origins takes some deserved hits, but it was also the first game I played when I got my GTX680 and was able to play with everything on ultra including the snow physics which coming straight from a 360 was a revelation. So I may have a fondness for it that others perhaps won't.