Don't limit missles.
If you're getting pounded, and you're eden, get some meteor defensis up!
If you're getting pounded, and you're plymoth, pound the person right back and get some spiders ready!
Honestly, I keep reading things in the OP3 suggestion section with people (including freeza) saying not to change things, and now I'm seeing people wanting to change this! You want to know a counter strategy? Here it is: emp your own units when the missle is launched! At the begining, make eveyone agree not to base-attack with missles! And for god's sake, use the forking spiders!!!! THey are in the game for a reason, take advantage of them!