That's a great point - people tend to overestimate how drastically the layout or design shifts between generations. Like you said, even when we moved from BW to XY, the card template stayed pretty consistent for a while. Mega Evolutions still followed the regular EX style, and you can see that...
I learned about pokémon in the 00's, every time I had breakfast before school they showed pokémon on tv. I found the episodes quite exciting compared to Shaman King back then.
Greninja ex works great with Chien-Pao ex for energy search and Radiant Greninja for draw. If Dragapult ex is a problem, definitely include Manaphy to protect your bench. You can also tech in Collapsed Stadium or Spiritomb depending on your meta. The promo Greninja can be fun for 1-prize trades...