Wouldn't that be a perfect reason to give it a second playthrough(ala remakes)? Though they were my favorites of the series to date, even I felt like the Hoenn story was flawed in some areas(one of the obvious things being their motives to a degree) and could do with some touching up. Along with the visuals being updated(which would serve Hoenn exceptionally well because of it's natural feel; Fortree City treehouses, Sootopolis City inside of a crater, the soot falling near Fallarbor Town, etc.) this could be an opportunity to erase (some of) that odd hate towards Gen III and for it to be more of an improvement than just visuals(which remakes should be anyways).
Just as Johto got some new areas(though I agree with others on that argument about HGSS not being needed but...yea), Hoenn also had plenty of inaccessible islands/areas located on the map that they could throw in some extras with.