Just taking a quick peek, for example if we look at .show()/.hide(): http://github.com/madrobby/zepto/blob/master/src/zepto.js#L5... http://github.com/jquery/jquery/blob/master/src/effects.js#L...
There is a major case where Zepto's technique just straight-out breaks: If you are showing or hiding anything that isn't a block element. This includes inline elements, table rows, or inline-block elements.
There doesn't appear to actually be anyway to unbind an event once you've attached it. Nor any way to detach all handlers of a specific type.
There is not a single bug fix for querySelectorAll - this includes the fact that querying from rooted nodes is completely broken for most cases.
I can keep going but yeah - there's a world of difference between Zepto and jQuery.
If you're only targeting bleeding-edge WebKit mobile browsers then yeah, Zepto might be fine. However in the jQuery project we take a far more pragmatic view of web development: There are more browsers than just WebKit and the market is much more complex. You can read more about it here: http://jquerymobile.com/strategy/