You might call this a change in house style. I don't know that I can confidently say that there were NO characters in the older Pixar movies that resembled each other. We see this with Disney too, in the way that most of the modern princesses have had their face based off of Ariel, Anna from Frozen and Rapunzel look similar, etc.
I think what has happened is that Pixar was originally going for realism, realism, and more realism, and a few things happened:
1.) Eventually there's a point where realism gets to be a bit too much, and so the decision was made to go in a more stylized direction.
2.) Lines have been blurred between live action and animation a bit more than average in recent years ("live action Lion King," anyone?)
3.) Perhaps the artists of Pixar simply got tired of the older style and are looking to try something different? As has happened in pretty much every animation studio out there. Not all Dreamworks movies clearly look like they're from the studio that made Shrek anymore.
It's a change, but I don't know that it's definitively a bad one. And it may well swing back in the other direction in a few films if the people at Pixar decide to shift it back for aesthetic reasons or simply because it fits the story better.