It had less to do with Pratt and more to do with it being a radical departure from the established voice of a very nostalgic and beloved character. It would basically be the same thing if Pratt was chosen to voice Micky Mouse or Bugs Bunny.
It’s also compounded by the fact that the Mario fan base, for good reason, loves Charles Martinet. Just see comments here for evidence. So pulling out a generic sounding Hollywood frontman felt like they were focusing on sales over source material. Which is true, but will always upset longtime fans.