As I have stated earlier that jQTouch is not a framework, it is plugin. Where jQuery Mobile is framework created for Mobile and tablet devices.
jQTouch is optimized for WebKit.Therefore jQTouch might be preferable if you plan on specifically targeting users tied to an iOS- or Android-based device. Where jQuery Mobile is compatible with all major mobile and tablet platforms.
jQTouch provides access to Geolocation (Access to device GPS Data) where jQuery Mobile doesn't provide this hardware access(to date).
jQTouch is focused on small screen devices. From their blog. "Apps developed with jQTouch will certainly run fine on iPads and other tablet devices, but we aren’t going to automagically convert to a more tablet-friendly UI that takes advantage of the additional real estate."
In terms of performance jQTouch is better than jQuery Mobile. If you are targeting only Webkit devices then go for jQTouch.
Though jQTouch project is technically active, the original author has moved on and development seems to have slowed where jQuery Mobile Announced in August 2010, it’s quickly progressed to a very functional Alpha 2.