Sizzle is actually a big one, CSS1 doesn't really cut it for anything but the most trivial use cases, although if you're only targeting modern browsers than I guess you can rely on their support.
Also, if you don't support each, I assume you don't support method chaining on enumerables?
As for actual missing features, the jQuery data stuff is really useful, but if the intention is to use minified with something like backbone, I guess it's kinda moot.
EDIT: I forgot to say nice library and I like the source code too.
My replacement for more advanced CSS features are the methods filter(), sub() and collect(). For example, instead of $('li:odd') you would write $('li').filter(function(v, index) { return index%2;}). But, admittedly, if you are well-versed in those advanced CSS features, they will always be easier to use.
You can chain list methods, as in
$('li').filter(function(v, index) { return index%2;}).set({$backgroundColor: '#000'}).animate({$backgroundColor: '#fff'})
to fade every second list element from black to white. The number of collection functions is limited to a minimum though. The Util module will add a lot more collection features (but at a cost of another 4kb).
Yes, that's true, data() is something I intentionally omitted because I don't think that it's worth its bytes today. For simple lower level effects toggle() offers a very different approach of handling state, and for larger apps you should use a MVC framework, as you suggested.
Also, if you don't support each, I assume you don't support method chaining on enumerables?
As for actual missing features, the jQuery data stuff is really useful, but if the intention is to use minified with something like backbone, I guess it's kinda moot.
EDIT: I forgot to say nice library and I like the source code too.