I only just heard about this, it was being explained in an interview how Desmond is actually the convergence point of many bloodlines which is what makes him special. That's fine, they're not retconning the plot as they never said Ezio and Altair was related, only that Desmond was descended from both of them.
The biggest criticism I'm seeing from people is "Well they obviously didn't plan this from the start." Which I respond with, so what? Not every story is fully planned out from the get-go, you can bet Shakespeare went through several changes for almost every story he ever wrote. The general outline may have been considered but all the finer details need time to evolve.
In short, even if they didn't plan this from the start, I don't see how that's a bad thing if it still makes sense and turns out to be a good story.