Here's how the initial paired versions, third versions, and remakes should be (and how FRLG and HGSS did it):
The paired versions set things up, introduce new Pokémon, etc.
The third version polishes the experience and adds new elements.
The remakes take the base of the paired versions, add the newer elements of the third version (when possible) and the game engine of the current Generation and puts them together.
Blue (the actual third version of Generation I) eliminated some glitches (though the
Blue engine was used for the international
Red and
Blue, we know not all of them) and changed the capture rates. These capture rates for the original 151 haven't really changed that much (barring some possible Legendary changes in recent years) and were in
FireRed and
LeafGreen.
Crystal added a few things, including female player characters, the Suicune subplot (with Suicune replacing Ho-Oh's place in
Gold, with Ho-Oh appearing later in the game in the same place), the Unown Dex, and the Battle Tower.
HeartGold and
SoulSilver had a modifed Suicune subplot, a replacement Unown Dex, the female player character (duh), and had the Generation IV Battle Frontier where the
Crystal Battle Tower was.
Emerald featured a hybrid plot between
Ruby and
Sapphire, but it isn't something that could be incorporated into the split versions. The differences really are having both teams be villains (with them splitting the activity they would normally do alone in their respective games), having to go to the Sky Pillar and encountering Rayquaza so it could calm down Groudon and Kyogre, the replacement of Wallace and Steven with Juan and Wallace, Gym Leader rematches, and everything related to the Battle Frontier. Most of
Emerald's elements (other than the Battle Frontier and Gym rematches) would have fit in making a
Ruby and
Sapphire remake.
I really do agree with this. We don't need to stop making new Pokémon, just slow down to a nice 50-70. This way they have more time to focus on a few, making them better (though that won't stop them from screwing up. Am I right
ugliest thing I've ever seen and
Special attacker with Moxie?).