To counter the fact of Mew being unavailable regularly, I'd simply make a hack for Emerald that makes event Pokémon available inside the game, and give it a rematchable Elite Four/Champion.
If I decide to get Mew in FRLG after all, I'd transplant the entirety of Faraway Island, or create an entirely new dungeon, and swap Mew with Jirachi (which will then appear in the Emerald hack). Neither Mt. Ember or Victory Road feel like places a Mew would hide at. Older versions of Throwback actually brought Faraway Island to FireRed. I have no flipping clue as to why newer versions lazily put Mew in Mt. Ember, makes absolutely no sense to me. I prefer keeping Mew in Emerald and giving Jirachi to FireRed, but an alternative could be to swap the two around.
Since I want to keep the games' close to each other, I don't attempt to make this a catch 'm all hack like Throwback or Complete Hoenn. It's easy to link up with the newest emulators. An alternative is PKHex. I tried many complete dex hacks in the past, until I realised the social element is what makes Pokémon. Without it, Pokémon is a mediocre RPG series in my opinion, that's only become worse recently, lacking RPG elements and exploration.
Hence why I'll make the same edits for LeafGreen.
Coincidentally, I resumed hacking today. I got Giovanni's stuff working. He will give you the Aurora Ticket upon defeat. Next I'll work on implementing a battle against the player character you didn't select (Leaf if you chose boy, Red if you chose girl). It remains to be seen if FRLG contains any vars/flags/special commands that change this trainer's sprite to the gender you didn't select, however. RSE does have it, for May/Brendan, but FRLG doesn't use any kind of similar trick.
This trainer will battle you in Cerulean Cave, spotting you on the path to Mewtwo. (S)he will give the 'Meteorite' item upon defeating him/her. Meteorite will change the layout of Altering Cave, making Jirachi appear in there.
After that I'll focus my efforts on a Prof. Oak battle in Pattern Bush. Upon defeating him, he gives the Letter key item, which, when given to Lady Selphy on Five Island, will activate the Celebi event in Lost Cave.
Finally, I decided to make Entei and Suicune guardians of the Ruby and Sapphire. They will initially look like the 'rewards' for reaching the end of Mt. Ember and Dotted Hole. Upon defeating/catching/fleeing from them, however, you'll see they were guarding the Ruby/Sapphire.
Raikou will be inside the new dungeon near Seven Island, Offshore Platform. Tanoby Ruins will now contain a new room (only accessible after solving Tanoby Key) containing an old woman, who, upon showing her the Legendary Beasts, will give you the Mystic Ticket, leading you to Navel Rock.