It's a dang catch-22, as they're screwed no matter what they do. If they add more Pokemon, they're in trouble. If they don't, they're in trouble. If they make remakes, they're in trouble. If they don't, they're in trouble. If they omit Mega Evolution they're in trouble, and if they add it they're in trouble. I wish Mega Evolution was never made a story point, because all the problems we're looking at are caused because Mega Evolution only exists in one timeline and does not exist in the others. They should have just made it a minor thing, and even then it would have caused problems because then we'd be asking why the villainous teams never use it.
This is one reason why I suspect that ORAS weren't originally planned to be remakes but instead, sequels. If GF knew from the start that they would be remaking RSE in Gen 6, I seriously doubt they would've set XY during B2W2's time.
From where they were going with XY, it would've made
far more sense for ORAS to be sequels set during B2W2/XY's time, possibly also paired with a Virtual Console release of RSE. Then, they could've put Megas and Fairies in Hoenn without having to introduce another alternate timeline (which was mostly done in the first place to explain why Megas and Fairies were in Hoenn, but not Kanto, Johto, Sinnoh, and Unova), and the continuity of the games wouldn't have been nearly as broken.
If this was the case, it's unclear why GF scrapped the sequel plans for a remake (although, the
3DS's issues with emulating GBA games may have been a factor; without RSE fresh in memory and readily available, a sequel couldn't have worked nearly as well).
With that said, I think the dissonance has to do with nostalgia. Back when R/S/E came out most people who played it grew up with R/B/Y and G/S/C, and they didn't like it because it wasn't as good as those games. The kids who grew up with R/S/E though liked it, and as the older fans became more sporadic the demand for an R/S/E remake grew, because they wanted the game they grew up with.
Personally I grew up in the third generation and loved the games to death, and you couldn't get me to play ORAS if you gave me a million dollars. To me, they changed too much of what made the originals great without adding anything in return, ironically much like the third gen games were like in comparison to Gen II.
Another big thing that hurt RSE's popularity back in the day was the fact that they had the misfortune to come out right after the Pokémania Fad of the late 90s/early 00s died and a
huge anti-Pokémon backlash started to set in. The entire franchise had become radioactive for anyone over the age of 10, which, alas, was how old most of the original fans were by 2002. Kids that age were expected to either move on to "mature" games like GTA or abandon video games altogether. (I, myself, became obsessed with the Sims.) To still be playing Pokémon at the age of 13 was to be wearing a giant "Kick me, I'm a dork!" sign on your back.
It started to change by the late 2000s when Pokémania reached its 10th anniversary and the original fans were all now 17-22 years old (a time when you start to care less about peer pressure and looking "grownup"). People started whipping their old cartridges out and getting nostalgic, and they were eventually rewarded in the form of HGSS. That exact same thing would eventually happen with the younger Gen 3-era fans later on, and ORAS were their reward.