At the time of this question being asked:
PokeTransfered Pokemon cannot participate in rated battles.
You can always breed them if you want them to participate. They need the blue checker symbol before they can participate in Rated Battles.
May 12th to July 14th, 2014:
PokeTransfered Pokemon can participate in rated battles.
In Season 4 of rated battles, any Pokemon except the following can participate:
Mewtwo, Mew, Lugia, Ho-Oh, Celebi, Kyogre, Groudon, Rayquaza, Jirachi, Deoxys, Dialga, Palkia, Giratina, Phione, Manaphy, Darkrai, Shaymin, Arceus, Victini, Reshiram, Zekrom, Kyurem, Keldeo, Meloetta, Genesect, Xerneas, Yveltal, and Zygarde