The effectiveness of mutas is very dependent on how many bases the Zerg player has. So if they're giving you trouble, your best bet might just be to be aggressive and keep him on 2 or 3 bases (while you're on at least 2)...and of course keep tabs on what he's doing so you can catch that spire building and get enough anti-air to handle the small number of mutas he's building. (It's small because he's not saving up a thousand gas because he needs it to defend your aggression.)
Also people you do understand that whenever someone says "If a grandmaster can do it then its balanced." or "You are not Grandmaster so you are a noob about balance." Is actually ignorant right?
Grandmasters have probably practiced and practiced and practiced and practiced to BARELY make something work. I have seen so many pro games where the smallest mistake in micro cost someone the whole match and engagement. Just because someone who makes it work doesn't mean its balanced.
If every Starcraft tournament was won by protoss, you would call it imbalanced that protoss is winning because its overpowered. When in fact majority of it is from the player? This is a game but to defend against a strategy you are asking me to have PRO level gaming ability? Unless I have pro level gaming ability I can't speak on balance issues? That is really ignorant. Starcraft is dying because of this very fact. *sigh* Rant over. Tired. Sometimes things are just imbalanced. Instead of crying about a persons ingame rank think to yourself for a moment, "Could this person be actually giving sound information?" Just because its barely defendable doesn't make it balanced.
This is the thing that people are ignoring or even refusing to see. More often than not it is the better player who wins, not the race.
A good place to start could be nerfing regen a bit. As it is, mutas regen while in battle. It should be like Protoss shields. Only when the unit has been away from battle 10 secs will the shields regen. Should be the same for muta health.