This could be done from what I've seen across the net, but it'll take a lot of work... Firstly, you need to consider expanding the ROM. Which Rom you use is up to you, as the game are pretty much all using the same basic formula, and the sprites can be used from later games in early ones, so there's no problem.
Now, what I would do if I was you is get rid of all the gimmicks in the games. That should give you more memory, right?
So, stuff like the Game Corner, the Poketch, the Phone, Pokemon Natures, Berries... All of it, I suggest is scrapped.
This is because there is a lot of data needed for the rather large area you want to do.
I wouldn't suggest you put all the Pokemon in there, simply because some of them are rather lame, and there's wayy too many nowadays.
Stick to most of the 151 and add a sprinkle of the others in while you're there. Maybe you can get rid of evolving, and make each species just that- a seperate species that is related... [possibly some text in the game could tell us that it was theorised by a Pokemon Professor Darwin takes millions of years to evolve, and thus the world decided to be from then on...]
So, basically, strip down the game to its bare components. The bits we all like.
Battling, Healing, Catching.
Now, if you're going to make all the lands into one game, I have an idea. Get rid of all the restrictive paths, and change things a lot.
Rather than having obvious routes, there can be roads, which lead to safe areas from town to town. However, we can go into the forests [which I would think should work like long grass does normally... I mean, honestly, I'd just expect bugs and snakes in long grass...], and take shortcuts, which are more fraught with danger.
Then, people have two ways to play: blasting down roads from town to town, or taking routes through woodland, catching pokemon.