I've been using Mootools for the last couple of months without knowing that MS was including JQuery with their new releases (like MVC). Now I'm not sure if I should switch to JQuery considering that I will be developing on MS tools and frameworks for the next years. I would like to hear from more experienced developers.
You need to evaluate whether the framework fits your needs. Knowing that MS has included jQuery may influence you towards that framework if it fits your needs. If it won't work for you, though, it doesn't matter who endorses it. That said, I have switched from Prototype/Scriptaculous to jQuery and I'm pretty happy with the change.
Note also that you can use jQuery in noConflict mode (and "extreme" noConflict) if you find that you have a need for things from other frameworks.