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Well...

I'm thinking that the Zero System would trump the Coordinator abilities. Coordinators are able to process data extremely fast, and have excellent reaction time. But the Zero system inputs data from possible situations that have not yet even occurred. It essentially allows the pilot to see several possible futures simultaneously. Granted Kira is also a Newtype and has SEED abilities, so that roughly balances out, maybe...
After that I would say that the Strike Freedom would hold the advantage due to the Dragoons. Though the Wing Zero has the Twin Buster Rifle. This gives a very wide and powerful beam spread, possibly allowing Heero to destroy the Dragoons before they can close to close range.
The Strike Freedom still has 2 beam rifles, 2 rail cannons, and the chest mounted beam cannon. So while it has more than twice the number of ranged weapons as the Wing Zero it's power is more than likely roughly equal. Both suits are equipped with beam sabers, and both have great speed and maneuverability.
I'd say that overall it would be a close fight, the fact that Kira does not kill and that Heero would have no reservations about it might give the Wing Zero a slight edge.

hunter zero i totally agree. Milliardo would kick both their asses. also considering he beat 4 gundams by himself while controlling md's, that takes serious skill. Also Stoic kira is not a newtype, he is a coordinator, a dammed good one but not a newtype. Mu is a newtype of the seed series. but anyways milliardo also comments later in wing that the tallgeese is reacting too slow... WTF? kinda sad that he gets that good, lol. but out of kira and heero, well i gotta say heero. and i don't know why you guys keep saying that strike freedom's weapon all together would equal wing zero's. that is incorrect. Wing Zero's twin buster rifle blew up a space colony in one shot.... there is no way in hell strike freedom, even firing all its weapons at the same time could have the same result. Also you are all forgetting that Wing Zero is made out of gundanium alloy of the wing universe which is ridiculously light, strong, and is naturally beam resistant. And due to kira's qualms about killing... well that is just a big disadvantage for him. Also i have a random question for you all. if Kira(which i am not saying he isn't, cause that is what he was meant to be) is the ultimate coordinator, then how is it that Athrun can fight just as well as kira and yet Athrun, is not special in the aspect that he was not meant to be the ultimate coordinator or anything like that. He was born and altered like the rest of the coordinators, and yet he ended up being just as strong as kira.

Go Heero Yuy!

gun gray did you even pay attention to what was going when that happened to athrun? first of all Athrun was not trying to fight kira at that point, he was trying to talk to him, if athrun was actually trying he would have been evenly matched with kira. and the only reason kira was beating the s**t out of everybody, was this. Yes he is skilled but he took advantage of the confusion of the strike freedom fighting both sides. and because of kira's stupid a** one of my favorite character in seed destiny died. hien westenfouse. the pilot of the orange gouf ignited. and to zetao, quatre did not control the zero system he went out of control with it. only zechs and heero can control it.

OK WTF? How is trying to figure out what the hell is going on, and just happening to be in the wrong place at the wrong time disgraceful? He was an amazing pilot. He was beating the s**t out of Gaia gundam without even trying. Give the damn man credit where credit is due. I don't even like kira. Somebody who is so against fighting should not e in a giant weapon designed for the sole purpose of killing.

...Uhm, this might stray off a bit but what about the M.E.T.E.O.R system? Im not saying SF is my top choice but considering the fact that its an added bonus for Kira, doesnt he get the slight upper-hand semi-what against the twin buster? (I'm just listing off advantages and disadvantages.)

They're both way too overly powered, which is why I need to watch gundam 0080, or the 8th MS Team which isn't about who has the most power and more about strategy (I think)

ok.... WTF!!!!!!?????? do you actually read posts or just skim through until you find something you like? oh and Maverick, they are not really that overpowered when you look at the technological difference between a series like 8th ms team, and seed or wing. they are only overpowered because you are comparing 2 completely different series.