I, for one, can certainly understand the sentiment that NEAQ is a let-down, and personally I rank it near the middle of facilities I've visited.
@Spike is right that they don't have all of the same "star power" many other aquariums have, for better or for worse. They lack large sharks (except for the new nurse shark!), there are only two species of penguin and they lack underwater viewing, and the only mammals are two common pinniped species housed in exhibits that leave a lot to be desired, one of which located out of the way in the back of the aquarium.
The big issue I have with NEAQ, however, is that it has some of the worst crowd flow and layout of any facility I've visited, and the fact it is always crowded makes it nowhere near as pleasant of an experience as it otherwise would be. While I have nothing but respect for the institution of NEAQ and they do a lot of great work trying to breed aquarium fish behind-the-scenes, I'd personally choose to visit a more enjoyable facility, such as Mystic or one of the zoos, any day of the week.