2) Testing costs. For larger sites it's not a trivial thing to test and support two different versions of jQuery. For any site that still needs to support IE8 (and 7 and 6), it will not be feasible to test and support two different versions of jQuery. As such, we'll never get the benefits of using jQuery 2.0 and would not be able to do so for many years.
3) Plugins will be written that only work for one of the two versions (1.9 or 2.0). This will divide the plugin ecosystem. Ideally, plugins should work for both, but many people will only test and support their plugins on one of the versions.