I could definitely see that happening, one of the biggest (if not THE biggest) complaints about Hoenn was about the lack of a variety of Water-types in the large swathes of water in the region. Every diving spot had the same three Pokemon in it (Relicanth, Chinchou, Clamperl--I still remember because of how repetitive it was). Going by previous remakes, if Gamefreak were to change the Pokemon encounters for any region, as they have in previous games, the water regions would be the best place to do it.
Also the biggest paradox in a Pokemon game so far that they have yet to fix is from RSE: Pacifidlog Town is built entirely on a colony of Corsola, but you can't find any Corsola nearby, even though they are present in Hoenn in other areas.