Earth Ship
This ship's missile was a subject of discussion before and I had mentioned some general ways of dealing with missiles like point defense, electronic warfare, and the speed and maneuverability of the missile itself. I still haven't had a chance to play Super Melee much, but after having briefly seen how this is working there are a couple more specific things I can say about this now.
An indirect way of making the Earth ship less effective at the retrograde it uses to make this missile seem so powerful would be to just lower the ship's turn rate by a lot. This one change alone will make the Earth ship seem much weaker. The Earth ship feels so powerful because the player is doing a classic Kaufman Retrograde, controlling the range flying backwards. It's even more pronounced here because the Earth ship's missile is about the longest range weapon in the game. So you can "hover" flying backwards firing missile after missile until the enemy dies and they can never even shoot back at you.
If it took the Earth ship a long time to turn around to fly backwards in front of the target the ship would feel a lot weaker. If you combine this with shortening the range of the missile so that most ships can shoot back in this situation, the problem will be mostly solved without needing electronic warfare or point defense.
And, of course, the missile itself could still be given a reduced turn rate, which would make it miss more often.