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Nope, I replaced my Empoleon with a Blastoise because Empoleon is a bit slow for me and his type is just dumb. He is Water/Steel so every time my opponent uses fire on me it deals normal damage which is pretty much ouchy But I must admit my Empoleon is probably the one who carried me all the way...
I didnt have any problems with the Gyms but in the Elite Four, Cynthia's Garchomp kept pwning me. I was only able to beat her because her Garchomp missed and I used Destiny Bond using my Gengar.
for me probably Giratina, I got so annoyed with him that I used my master ball on him.
I caught Dialga with a quick ball and Palkia with my 4th Dusk Ball.
Tip: Get a dugtrio and use him against zapdos. His ability prevents zapdos from fleeing and dugtrio is completely immune to zapdos' attacks.