They are both completely different decks, you can't really swap them out for each other.
Palkia G is really a Power lock/spread/snipe deck that runs 4 Mesprits.
Dialga G is really a tank deck that relies on Sp. Metal to build a Pokemon that NEVER DIES.
Since RR came out, both decks have serious counters. Dialga G can't tank against Infernape 4, no matter how many Sp Metal you put on it. Palkia G has trouble working without the LV X so it is vulnerable to Flygon (especially if it is Palkia/Alakazam), as well as Luxray GL.
Most Palkia G decks had a 1-1 or 2-1 Dialga G teched in them anyway. if I were you, I would have another go at running them both in the same deck.