Tough choice. I can't really make a decision based solely on Tali, either.
The Quarians did make a huge mistake in attacking the Geth first once they realized they were self aware. Granted, the Quarians then and the Quarians now are probably very different.
Eh, I'd probably go with the Geth. They'd got more numbers and they seem like they'd be more useful in the long run.
The ideal thing would be to try to broker some kind of truce and put the events of the Morning War to rest. Legion does imply that the Geth wish to make peace and regret killing so many Quarians in the war, even if the Quarians did start it. You just have to get the right Quarians to speak up for peace.
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Gamertag/PSN-Murphiroth