I've been using Prototype for years and am now using jQuery more, and I have to agree. The knock against Prototype was that it modifies built-in classes, but I seriously doubt how much that actually matters, and as a programming library it makes much more sense to work with, I think. jQuery doesn't even offer very useful things like list comprehensions! You have to use underscore to get those.
Actually, splitting out logical code from DOM manipulation code makes plenty of sense. Just because I'm using one does not mean I want the other and both stand on their own fairly well. This is even more important now that JavaScript is popular on the server--I can use Underscore there as well.
