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I would like a Bug Type for my Emerald Run. So far I have a Mudkip and I'm thinking of getting a Ralts and Makuhita, so should I even use a bug type?

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I may not get ralts, i am thinking about it though i will get makuhita
Don't listen to him or her go with beautifly it's very useful I used it from the beginning of the game till the end and it was a big help and the Pokemon League. Beautifly is currently level 70 anyone who thinks it's not good just didn't train it good enough.

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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

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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

enter image description here

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.

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Flash is an HM in Emerald