I had a look at Backbone.js and while it's a great product, I don't like the binding to jQuery/Zepto for Controller navigation.
I know that I can use things like Models/Collections in Backbone without jQuery, though I do want to use the routing in Controller and not reinvent the wheel myself.
So my question is whether there are any lightweight MVC frameworks which are preferably JS-framework agnostic, or, in worst case, support Prototype/MooTools?
Backbone's jQuery integration is just a light dependency -- it's not required. If you don't want to use Views or Controllers (i.e. -- no DOM Manipulation or Ajax persistence), and just stick to Models and Collections, you can use Backbone perfectly well without including jQuery at all.
Jerome Gravel-Niquet also has done the legwork to build a version of Backbone that's backed by Mootools instead of jQuery:
https://github.com/jeromegn/backbone-mootools
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