Why do FR/LG just cease to exist in the timeline now?
Because, ORAS established the existence of a new timeline where Megas and Fairies exist, so none of the first five Gens are part of that timeline. Remember that the Hoenn story is supposed to take place at the same time as Gen 1 Kanto...
I think that Kanto overall is the less developed of the regions. Even GS Johto felt more developed to me from what little I played of it compared to FrLg Kanto but then again I didn't play the originals... they didn't even develop Kanto though in the Johto remakes though...seems Kanto will always be the simple region out of the five...GF is thinking of going 'Simple' with Gen VII according to an interview they did some time after XY came out...honestly if they plan on doing that they may as well remake Kanto...
There's nothing inherently bad about simpler stories (in fact, I much prefer Gen 1's simple, yet realistic story to Gen 3 and 4's attempts at going "epic" with heavy-handed mythology, "god" Pokémon, and the like), but there was still a lot of room for improvement.
Even if FRLG weren't Yellow Remakes, I would've liked to see Jessie and James return. Aside from being an easy, convenient way to introduce double battles into Gen 1, they also had a lot of potential for further development. Why didn't they return in Gen 2? Did something happen to them when Archer took over Team Rocket? We could've gotten a little bit of the Grunts' perspective on how their employer treated them (which, I imagine wasn't well), and Jessie and James would've been developed into distinct characters from their anime counterparts.
And, what about Mewtwo? Why and how did it destroy Cinnabar Mansion, and why was it in Cerulean Cave? And, most importantly, who created Mewtwo in the first place? Was Team Rocket involved? There was *a lot* more they could've done with this.
And, everything about the Sevii Islands. If you're going to go through the trouble of making a brand new region for FRLG, then do exactly that. Why couldn't they have had some gyms? And, I wouldn't have minded seeing them take a page from the anime and introduce a connection between Articuno/Zapdos/Moltres and Lugia.
And, then, there's the gameplay-related stuff. There was absolutely NO excuse for getting rid of the internal clock, let alone day/night. Yes, the originals didn't have one, but FRLG were supposed to be
3rd Generation games. They might as well have gotten rid of held items, abilities, and natures.
Same goes for berry trees. GSC had already established berry trees as existing in Kanto, so why suddenly get rid of them? Again, FRLG were supposed to be
modern remakes, not Red and Blue with 16-bit graphics pasted on.
And, the Pokédex. Gen 2 Pokémon are just as much a part of Kanto as the Gen 1 ones, so why restrict us to just the original 150,
to the point of not even letting us evolve Golbat? What was so bad about giving us the first 251 (plus Azurill and Wynaut)? At the very least, could we have gotten the
40 Gen 2 Pokémon that were originally planned for Red and Green?
While FRLG have their fans, many people (myself included) found them to be very disappointing remakes. There were just way too many missed opportunities with those games, and while it's good that GF seems to have learned their mistakes with HGSS and ORAS, it's a shame to see the beloved 1st Generation stuck with such underwhelming remakes. I think they deserve better than that.