Neither of them are going to be of use in Gym Battles, being weak to half of their types, and aren't really of any use at all, so you may want to consider a different Pokemon. There is no prblem in using them though, so I'll compare the two.
I won't be taking stats in to account much, because this is in-game.
Beautifly
Pros
- Learns Giga Drain, which is useful against Juan
- Has a reliable form of recovery
- Leans Stun Spore, which is useful for catching Pokemon
Cons
- Shallow movepool
- As I said, not much use against the Gyms, other than the Psychic Gym.
- Doesn't learn any HMs
Masquerain
Pros
- Stun Spore
- Flash
- Intimidate
Cons
- Very shallow movepool, relies mostly on TMs, which are one time use in Emerald
- Doesn't learn any HMs
- Only really useful against one Gym, the Psychic one
Their cons are basically the same really, but Masquerin has a worse movepool and its other pros aren't really that useful either, so I would say Beautifly is the best choice. Other than that, there is aesthetic qualities, but that is based on your preference. Although Beautifly is the best choice, they don't differ that much so if you like Masquerain's design more, by all means go for it.
Type wise they don't unbalance your current team.
