>When Unit01 was swallowed by Leliel in 16,
> Unit01's return was top priority.

This is what sparked this off in my head. They were prepared to go to any
lengths to get Eva-01 back, even possibly killing the pilot. If they'd used
a production Eva it wouldn't have mattered as much.

Also, Shinji is a rather dangerous pilot for Eva-01, since he tends to go
berserk and ignore orders. If they used a calmer pilot such as Rei (who,
incidentely, does go rather blood thirsty in battles IMHO, which is
uncharacteristic of her) then Eva-01 would stand a better chance of
surviving. Maybe why they tried those cross-compatibilty tests...