The
ending seems glitched since you can activate it with only 7 villains captured out of 14, but if you get like 12 or 13, then you seemingly have to get them all. I still need to test it out since I've only completed all side missions before activating the protocol.
That said, you only miss out on two cutscenes it's not ideal of course, but watching them on Youtube is the same experience. Don't put yourself through content in a game you don't like just for some FMVs. If you unlocked new characters or game modes for getting 100%, that'd be one thing, but it's just a video. You beat the game, you just didn't 100% it you miss out on post-capture villain dialogue here just as you would in City with the Riddler.