First of all Shinn is not a super coordinator(i take it that you mean an ultimate coordinator). Kira is the only one of that kind and because of that stands highest on the coordinator mountain weather you like it or not. Kira got the genes to become the best which you probably have seen. It's not just the unit, it is Kira's skill to.
As for the DRAGOON system used how Kruuze did it. That is not cheap, it's using your resources to the fullest and attacking through tactics to take down your opponent as easily as possible. Much like Shinn did with the Impulse.
You are also forgetting that SF is not Providence, Kira got a number of possiblities to attack and if he truly has become a newtype Shinn won't stand much of a chance. Shinns piloting is rough and he hasn't mastered mobile suit battle to the extent Kira has. Kiras piloting is much more flowing and if he commits to taking down Shinn i can't see any reason why he wouldn't succeed.
Try looking at the facts and the way they use their suits. Don't go by what you want to see.
There is also the plot that is preventing Shinn from defeating Kira again. He has done it once, he won't do it twice. There simply isn't room for it unless Shinn turns evil which i doubt will happen.
Now i'm not fond of Kira's newly aquired powers but they are there and you shouldn't close your eyes to them. If you do it will be to much oc a chock when Shinn falls.