Sure the prequel game was developed after, but canon chronology speaking, Ven's very important and irreplaceable. He's(as far as I know) an ordinary guy who was in the wrong place at teh wrong time to get picked by the f***ed up master that is Xehanort, then got his heart torn in two. Sure, it *could* have been someone else, but the circumstances make the character. Aqua and Terra could have been two differently designed/originated characters, but they are unique because of what role they play.
I'll somewhat concede on the Vanitas thing though. I feel like they could have done more with Vanitas' character, but he's not completely useless either. Van is evil, but it seems like he was just a secondary add on villain without any outlined motives to his actions. Was he complying with MX's wishes because he wants to, or does he also have a bit of his own motives? I feel like it would have been slighter cooler at least, if they kinda gave Van a bit of his own autonomous thought, a little like how Braig acted with MX.
I second the person that said Xion feels a bit like the useless one, or at least, a badly constructed character. She could have been more "useful" seeming if her story was designed better. But that's just IMO.