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. Thanks!
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.
Considering that Microsoft is also providing free support for jQuery as well, I think yeah, you should give it a try.
Personally, I wouldn't switch to jQuery from Mootools if you paid me, but that's because I prefer Mootools' framework approach over jQuery's toolbox approach. Your mileage may vary, of course; particularly if you just need a really fast way to get amazing transitions and Ajax up and running jQuery can be great. A wonderful article comparing the two is here if you need a really thoughtful comparison: