First of all, Pokémon from Pokegen are not always the problem. If on Pokegen, you make them legit (meaning no more than 510 EVs total; 255 EVs per stat, hacked move sets; Vaporeon with Blue Flare, etc.,) you can use them.
Second, they don't allow legendarys. (Mewtwo, Mew, Lugia, Ho-oh, Celebi, Kyogre, Groudon, Rayquaza, Jirachi, Deoxys, Chatot, Dialga, Palkia, Giratina, Phione, Manaphy, Darkrai, Shayin, Arceus, Victini, Reshiram, Zekrom, Kyurem, Keldeo, Meloetta, and Genesect.
Third, you cant have two of the same Pokémon.
Fourth, The moves Sky Drop, and Dark Void are banned.
Fifth, double items are not permitted.
Sixth, Pokémon Abilities/Berries that have not been released yet are not allowed.
Hope I helped! ~Jigglypuff323