Going by Mahq.net, there's been a dramatic leap in performance for Valks since the VF-1, even if the weapons haven't changed much. The difference between the VF-25 and the Queads wasn't particularly pronounced, even accounting for the pilots. Going by the stats on the site, a VF-01 would have had roughly a tenth of the ability a VF-25 has, with the difference not being as exaggerted at low elevations while in an atmosphere.
The conclusion I've reached is that all the times Queads fought VF-01s it was below 30,000 meters, while in space VF-01s would have absolutely gotten slaughtered.
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