Shifts in tone are not necessarily bad; in Toy Story, they worked. Pixar has always been a bit of an envelope-pusher, not in the actually-quite-safe-nowadays sense that Hollywood "pushes the envelope" by being increasingly raunchy or otherwise inappropriate (or pushing a political agenda popular in Hollywood that they pretend makes them mavericks), but by actually trying new things, artistically.
Pixar also actually, to my understanding, has an incredibly sweet deal in terms of their liberty and self-control. Recall that Pixar was originally a sub-division of Disney that then later was successful enough (but not quite the direction Disney thought they wanted to go) to split off. When they re-merged, it was because Disney was back in an acquisitions cycle, and Disney saw Pixar as doing really well. Pixar was asked to come back, and got elevated beyond being a sub-division. It's called "Disney-Pixar" for a reason, now. I don't think Disney has quite the level of control to arbitrarily move management around that they might with other properties.
That said, Pixar making sequels is not a bad thing; their design model is CGI, and so re-use of actors and sets is an enormous money- and time-saver. And pushing the design envelope to try out other "feels" that their settings can give is fine, so long as they don't go so far off kilter that it's "just weird." As, apparently, Cars 2 and MU are. (Notably, it could be that some of these will become favorites of different audiences who found the originals to be not to their taste, so it's an interesting approach.)
In short, I think Pixar knows what they're doing, and are not doing it cynically but with an eye towards being originators of new models of movie-making.