Hands down, I'd say right now Emerald is the better choice, especially because of pokeemerald decompilation project. There are far more possibilies with Emeralds now than FireRed. Dizzy's and KDS's Hacked Engine, Battle Engine, Item and Pokemon expansions are one of the best features in Pokemon ROM-hacking, as well as ongoing decompilation of Emerald. So, yes, I prefer Emerald as for now.
Ok, but do you recommend me some emerald base rom with pokemons from the latest generations, mega evolutions and etc?
As far as I know, there isn't any good rom bases for Emerald, but for megas, Pokemon expansion you may install Battle Engine Upgrade, Dizzy's Hacked Engine and Pokemon Expansion from Dizzy and ChaCha DInosaur (KDS), and insert new Pokemon yourself. But if you're confused, you still can use FireRed for beginning. There is the Leon's and UltimaSoul's FIreRed Rombase which I guess is far more friendlier for beginners than all that Emerald stuff. So, it's for you to decide.