@Isaac
Well, it's Rayquaza. A dragon-flying type meaning that almost no hero-partner combo has a real advantage against him if they use their STAB moves.
And... You didn't know about the post-game recruits? Have you ever beaten Mystery Dungeon's story?
@Kristia
I'm just remembering the number of times I had to fight Groudon over and over in an attempt to recruit him. In an older save, I had most dungeons unlocked and post-game content done but I could never recruit Groudon.
Spoiler

"Why won't you join me, Groudon?! Why?!"