Jake Pentecost definitely wouldn't have existed, and John Boyega would've never been considered or approached the role. Hell, Pacific Rim wouldn't even be the same movie (chances are, with Cruise in the role, he would have the story focus more on him).
Honestly, I don't think "the son of" character angle would come into play at all. John Boyega's Jake character exists only as a lit. replacement of Idris Elba's Stacker Pentecost, who died. His popularity at present is also one reason why Uprising was made at all (it would've stayed shelved otherwise, I think).
If they had gone with Tom Cruise as Pentecost, I think a lot of the original script (where Pentecost lived) would've been its base work. Chances are, Cruise's character would remain the focus of a sequel with new characters in addition to Raleigh and Mako.
The final movie, definitely. del Toro and Beacham took the best ideas of the original script and completely reworked the frame itself, for the better I think. I'm not particularly upset that Stacker Pentecost died, it worked for the story they were trying to tell.