I agree. The plot was flimsy from the start. It buckles at the very premise of having a portion of the city turmed into aprison run by a super villain.
You could see why they did it though: they wanted to put batman in a city setting without dealing with the consequences of an actual city. Like: innocent bystanders, cars...etc. I appreciated the villain cameos but as a result, and because of the source material. None of the characters have much depth. That said gameplay is great...

I actually think the Infamous games are much better. The writing in those games is always engaging and interesting, and the characters are generally well developed.