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I've done the same thing, sort of. But I'm trying to get back into rails more and the fact that they're in bed together (rails/proto/script) keeps me from swearing off prototype for a while. I've used Prototype in some Java apps and jQuery in others and I definitely prefer jQuery for handwriting the code, but if someone out there can make jQuery a first class citizen in rails (I know it's all open source, but I ain't doing it :) ), I'd have no problems waving the white flag on prototype.

Digg.com actually uses both, which are the two largest page elements when loading any digg page.

I don't know, I thought crap was the largest element on any digg page. Zing!

As far as keeping HTML clean when developing in Rails, there isn't any need to use Rails' AJAX helpers if you don't want to. I learned how to use Prototype before I learned Rails and I'm still very comfortable with just writing straight Javascript instead of using the helpers. So if unobtrusive Javascript and unmuddied HTML is the goal, Prototype still fits the bill.

Too much damned AJAX, not enough work on browser launched or hosted Rich Clients!