I like emerald better, and honestly it's suprising I don't see enough ROM HAcks using emerald as a base especially to remake the original Red/Blue considering how similar the Hoenn Map is to the Kanto Map. One can easilly make a Red/Blue remake using emerald and end up having the benefit of a few extra towns along the way and with it also better locations for the legendary birds and so on. Plus Emerald as a base for a Red/Blue remake works even better with the emerald version's berry system, what with the EV berries. Emerald's breeding system takes a lot of the headaches out of getting the right pokemon with the right moves and stats as well. We already have a 4th gen phys/special split for 3rd gen hacks thanks to DoesntKnowHowToPlay, I'm suprised more people don't take it a step further to enable the emerald berries and emerald breeding mechanics to the older GBA titles if they don't try a R/S/Fr/Lg hack on the emerald engine.
One can even add touches of the anime to a Fire Red/Leaf Green built on Emerald without making it explicitly an anime rom hack either, since the Winstrate's Macho Brace is very much similar to the training tool AJ used on his Sandshrew to name an example so one can turn the Winstrate's house into AJ's gym. Dewford Town is in the right place to put Cinnibar Island. Fortree City is around the right spot for Cerulean City and Mt. Chimney can be moved to Cinnibar Island to work the island's need for a volcano. And another anime touch would be how the Battle Frontier was in Kanto in the anime but each facility as scattered across the land akin to each gym. Other towns not seen in the original games can be made up to mirror some of the towns from a few of the Kanto saga's filler episodes which can end up being important like dealing with Snorlax for example. And honestly the concept of Grandpa Canyon in the episode Attack of the Prehistoric Pokemon was a very nice and logical idea considering that fossils are best found in places like that.
Despite these parallels I have seen no one try to take this idea and put it to work. I'd do this myself in fact if I knew how to do anything related to rom hacking and modding. I hope someone is inspired by what I said however, while I can't do any coding or whatever ideas are something I can offer and that can be just as vital.