Ruby's slightly different storyline makes more sense. "We want to expand the ocean so there will be more fun places to go swimming"? Really, Team Aqua? The best part is, that wouldn't even work. More water on earth would mean shorter landmass perimeters. Smaller beaches.
I probably won't skip it, but... what I'm thinking about is all the expansion-type stuff that the Third Version usually introduces. HGSS came after Platinum and had Move Tutors, the Battle Frontier, gym leader rematches and other stuff from it. FRLG came before Emerald and had nothing. I would have hoped for Hoenn to be Confirmed AFTER the probable Z or X2/Y2 or whatever. That way, I could have X and Hoenn Remake with all the ground covered between the two. Ultimately, the extra goodies matter to me more than the joy of needing a Fly/Rock Smash/Dive/Cut slave again, so if I'm right, maybe I can summon the self-respect to not bother with it.