Palkia's attack is good, but you need to discard 3 water energy. You're probably only using that attack once. Sometimes that's enough, but there are many times when they just bring in a second ex from the bench after you take down their first, and greninja cant chip away at their bench fast enough for you to take that last point. Gyarados ex can tank nearly any attack they use and ohko every relevant threat with its attack + greninja's chip. Palkia's 150 hp means it can be ohko'd by Mewtwo when Gyarados can't, and I think that matters a lot. Additionally, Gyarados ex can sometimes discard an energy from the benched pokemon theyre charging up, which can very easily steal games that were otherwise lost. Imo, Palkia is pretty heavily outclassed unless it gets good support in the set.