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The gym leaders shouldn't be impossible. You are going to have a team with level 15-20ish pokemon with moves like tackle, ember, and peck. Giving the gym leaders fully evolved forms of OU and UU mons with good moves and little cup ubers with strong items is just going to get the player...
I think that the water immunity abilities would be good as the only thing that they prevent from hitting the CAP is Keldeo as Greninja should have psychic type coverage to deal with the CAP. Another possibility would be Magic Guard to switch in and absorb will-o-wisp burns. This also...
Even unboosted conkeldurr can't really swich in.
252 Atk Adaptability Mega Lucario Close Combat vs. 252 HP / 0 Def Conkeldurr: 296-350 (71.4 - 84.5%) -- guaranteed 2HKO
followed by priority KO with bullet punch or extreme speed