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It depends on the equipment..

Strike Freedom + METEOR system > 00 Gundam + 0 Raizer

00 Gundam + 0 Raizer + TRANS-AM > Strike Freedom + METEOR system + SEED mode

TRANS-AM > SEED mode

TRANS-AM is the special mode of the mecha itself rather than SEED mode which is effective on the individual who has the special ability. Unlike a machine, a living organism will grow tire even if he or she is genetically modified to possess great potential. Thus, Setsuna F. Seiei has an initial advantage to begin with.

More over, Setsuna F. Seiei came from a place of war in which he grew up as an armed terrorist, killing for survival, not mentioning that he was taught and trained by Ali Al-Saachez, a mercenary known for showing no mercy to whoever it is as long as he is paid. On the other hand, Yamato Kira is a well-known pacifist who prefer to talk things out rather than starting off with a battle. Thus, psychologically.. Setsuna has the upper hand because his intention is murderous whereas Kira would like to resolve the battle through other means of battle initially.'

Setsuna has quite a high kill count, whereas Kira doesn't. In fact, most of the mobile suits Kira destroyed, it were either empty cockpits or the cockpits weren't harmed. Thus, to conclude my long analysis... Setsuna F. Seiei will win the battle!

kira definitely has higher mobile suit pwns per minute, setsuna takes like 5 minutes to pwn 8 aheads

so in "kill mode" kira would win

trans-am has time limit, kira can outlast, kira can force a long range battle and just dodge any attack from transam then wait till transam runs out and pick on a range attack defenseless 00

Personally i think Kira would win. Setsuna may have a higher kill streak but he cant match the amount of mobile suits Kira disarmed and in the time he did it, which takes precision since he is attacking crucial parts of the suit with out harming the pilot by an explosion, misfire or cutting to far with his sword. And even though Setsuna has the Trans-AM Kira could just counter that with SEED mode, giving him enhanced reflexes, quick thinking and overall better piloting skills, oww and theres the fact that he is a coordinator meaning he already has those skills and they will get alot better when SEED mode activates, Then again Setsuna could go all innovator on his ass, giving him the ability to read Kiras thoughts then again the probability of him being able to track his enhanced thoughts in SEED mode is unlikely, plus Trans-AM could just run out because of its time limit.