The solution to the "Stun Wars" is really simple, don't let the fights take place at close range. Use cover, long range weapons, snipers, etc to counter the "close and stun" tactic.
Yes, stun damage can be very effective. I had a character last session take out twelve minions with a couple of well placed stun grenades. Granted hey were minions, and were all in the same room, but it really was like shooting fish in a barrel.
I don't see that as game breaking. I see it as clever tactics, like a SWAT team with flash-bangs. The monster doctor with 6 Brawn, 5 ranks Brawl, 5 ranks Medicine, 3 ranks Feral Strength and Deadly Accuracy is going to burn a lot of experience getting that way. Experience that is not going to be spent getting better at other stuff. One easy GM counter is to design adventures and encounters that cannot be resolved through application of Iron Fist Technique. Slicing computers, social interactions, racing to find a cure for an alien disease, logic puzzles, mysteries, etc. or a good old speeder bike chase through the alleys of Coruscant.
The other option is to embrace that play style. My players mostly want to blow stuff up in an epic manner. So I write adventures with plenty of epic stuff to blow up. I am pretty sure that a player who wanted to game she system could create a social monster or a piloting monster, or just about any other narrowly focused and unbeatable in that one area character. If the player builds a hammer nothing says you have to give him problems that can be solved by pounding.
Reading the books looking for theoretical loopholes is one thing, but what shows up in actual play is often quite another.