There's no doubt only Mu knows the line. "But im the one who can make the impossible...possible."
Kira and Shinn both activated seed mode. In that way there is no question that there's no difference when they're all in seed mode. Athrun owned Kira when they're both in seed mode. Coordinators > Naturals because they have seed mode and even when they arent they've already acquired all their knowledge of battle tactics that they learned while in they're berserked and lived to fight again. Berserk= Berserk. The difference is who has better mobile suit and who is overall better pilot while in seed mode. There is no such thing as one seed mode being better than the other. The only difference is Kira > Shinn because while Shinn tried to kill Kira with everything he got, but Kira wont kill anyone unless he has no choice and didnt fight with all his strength. Shinn is a ruthless killer and if the situation was reversed, unlike Kira who let Shinn ran from this battle, he would have killed Kira like before while he was retreating. If the tables were turned Shinn would have killed Kira while he was running and defenseless. However, Kira > Shinn berserked. They both activated Seed mode. Shinn couldnt lay a finger on Kira even with a faster and deadlier battle suit. There's no such thing as a hybrid Mirage Colloid. You either see the thing or you dont and you could clearly see Destiny and its moving at a faster speed than any gundam, hence the afterimage when its moving. There's no comparision and if Kira commanded Destiny he would be unstoppable for as long as Destiny could stay powered up.
Kira almost couldnt keep track of Destiny's movement even in seed mode when such a berserker would have an enhanced sense of spatial awareness. Destiny > Strike Freedom. Strike was built for gunning down mobile suits but otherwise speed is one of the thing MS are made for and is one of the most important quality besides having a competant pilot who can use it in the first place. If we're comparing medievil roles Kira is the ranger and Shinn is the knight. Shinn's mobile suit is made for galloping in heavy armor and shield in hand into battle and while Kira's was made to gun down enemies with eagle eye accuracy afar but is not to be underestimated when having to go face to face and get close enough to know what the guy next to him just ate the other day.
I was surprised Kira could even catch Shinn's giant sabers with just daggers. He activated berserker almost simultaneously as he fully intended to catch Shinn's saber and disarmed him as he doesnt intend to kill Shinn which is why Shinn said "You mean that if it was a beam it would have been all over?" Shinn on the otherhand would give no such mercy. He couldnt do that without berserker mode because of his MS's disadvantages in the speed department. Otherwise you could clearly see that Destiny could just run in circle around SF and pick any enemy off and get away scot-free, no relation or offense to Scottish folks. They both activated their seed mode one right after the other but Kira owned Shinn even when Shinn has his giant two hand saber out while Kira already put away his two small swords for his guns and needed only daggers or rather apple paring knives to defend himself and took down a crazed and berserked Shinn without even sweating while Shinn completely drained his MS.
As for having unlimited fire power, it doesnt matter. Battles are won in an instance and Shinn had a better MS but he couldnt do anything to Freedom and had to drain his MS of even primary and secondary power and still couldnt own Kira when they're both in seed mode and Shinn has every intent of murdering Kira on the battlefield while Kira does not. Having nuclear power isnt everything. It doesnt make your suit better. It doesnt make it faster. It doesnt improve your pilot skill. It does however enable you to use your guns alot and move around the battle field for a long time. Even if Shinn has nuclear powered suits he would still take forever just to annoy Kira. On a good day when Kira is serious he's unsurpassed. I dont see why you Shinn fans like him and say Shinn was already into 66% of the battle or Kira went into seed mode first or Kira had better mobile suits. Maybe Nuclear power makes some difference but its not the be all end all quality that makes a mobile suit and it doesnt make it indestructable. Freedom can still be taken out in one stab or shot and if your shields are gone and you got no weapon then tough luck. As for the 66%, i hate numbers. However when Kira stepped if you look at the time frame it was like a few seconds after Cagalli started shooting and Shinn easily took her arms out. However Shinn was spending a good hr or so trying to kill Kira all over again, slashing at him, exchanging shots while Kira aimed Shinn's shot perfectly and nullified Shinn's shot effortlessly. Shinn's gunning skills could still need help even after Athrun teached him how to hold a gun properly and after years of military training while Kira starting holding gun and was never formally trained when he met Captain Ramius but was awarded Strike gundam instead of Mu. Kira is a natural warrior; Shinn needs to spend his whole life in the military just to do what Kira can do all while Kira just came out in the fresh from underneath a rock. This is what i like about him as he's not a ruthless killer nor one who is indecisive. I wish Athrun would make up his mind what he wants to do. It shouldnt require your former fiance to help tell you what to do with your life after your dad already done told you so and died for what he believed.
As for Kira haters seeing he has new-type ability, it's not an ability so much as a premonition. It doesnt make you unstoppable like you think it would. It does so something but so far the writers have shown that all it can do is tell you that the main characters notice each other's presence. Mu has it whenever he felt raww's presence. Its like, hey i dont know that guy but i think he's up to no good. Kira's new-type was activated almost simultaneously as he shot down the goufs that were chaining him down to disable his MS body parts. It didnt enhanced his shooting skills, accuracy, or anything. He just knew they're not friendly coordinators and his shooting skill is already unsurpassed. He knew this even beforehand when he stepped into the battle against Dullindal's goons that were attacking Lacus and that he had to take them out before they take him out. Maybe it is an advantage in that you wont shoot friendly MS but in this day and age technology is advanced and new-type is an obsolete ability. You can store a thousand databases of enemies and friendlies in those MS's and keep track of when they're coming a mile away. Seriously, new-type is just a way for the director to show something flashy on the monitor so that the audience doesnt get bored of all the senseless violence thats going on. I dont know if its different in Japan but here in America GS universe would be rated PG-13 for animated violence and nudity.