Eh, Torch became Captain America. Sheldon's Dad became Leonard's high school bully 10 years after his death.
Point being, and I believe a lot of comic book roles can change and still be great, but Fantastic Four was the first family. Reed Richards needs to be smart, but needs to be clean cut and wholesome as well. Pedro is a fantastic actor to be sure, but clean cut and wholesome is not exactly his gig. It's not like we are casting a popular comic book character that the real world is not so familiar with.
John from The Office fit the picture physically, but I don't think he can pull of being a genious. Especially after Dr. Strange.
But, these are different times and maybe what should be shouldn't be. I thought Heath Ledger was the worst casting ever until The Dark Knight came out, so what do I know.