Though it isn't listed, my all time favorite Pokemon would be Celebi. It can travel through time. It has nice base stats (though not the greatest). It was as nice typing in it's original gen when bugs moves weren't popular *cough cough* Megahorn *cough cough* and Darks were barely introduced. Another reason why Celebi is my favorite, is it's rarity. Outside of Japan, Celebi is not common at all.
Mewtwo is probably my favorite, I love Psychic types and he is no exception. Mewtwo also has a great backstory and is very powerful and hard to catch. Darkrai, Lugia and Rayquazza are also some of my favorites.