The problem is that there's some games that can't be emulated. That includes basically all 3DS-on games, and certain versions of Gameboy games (i.e. Emerald) don't work on the Gameboy emulator.
Really, the only games I had problems emulating were HeartGold and SoulSilver.
Come to think of it, it's the postgame that causes the game to freeze up (which sucks because that's the part I want to play)!
I experimented with the post-game on Emerald via emulation, and I really didn't find any issues. Granted, I didn't really play the Battle Frontier a whole lot, but still.