Here are some of my thoughts:

The guys that were with Papa, said "it seems to be a rare sample without signs of physical aging"(EP 2), they refer to Hiro not 002 because that line is followed by this one "It's Code 016. That's him, isn't it?" So piloting with 002 drains your life.

001 might be Dr. Franxx because he has one horn, he is also very old(aged faster than usual) and well, half robot. Also in the opening is a scene where 002 (red one) is holding hands with someone else, being in the past and because there is no 001 number in the opening it might make sense for Dr. Franxx to be 001.

Another thing that i notice was or actually were Nana and Hachi. In Japanese Nana means 7 and Hachi means 8. Keeping this in mind, in the opening we see two new numbers (007 and 008) and later on Nana and Hachi with censored codes.

As for the way they are piloting Strelizia, the difference is for sure, the depth of the connection between pistil and stamen. Can't think of anything else. Because it has the same cockpit, same suit, the mech talks with the girl voice like everyone else, Hiro had the same feeling he had in Strelizia when he was in Delphinium (one of the reasons why it stopped working for sure).

Did you guys saw that the gauge between Goro/Ichigo went to 102/102( kind of slow) but between Hiro/Ichigo went to 100/100 (but fast). Maybe Strelizia gauge isn't the same? It needs to get higher because 002? Not matching 002 means you get devoured?
“If you don’t belong here, just build a place where you do. If you don’t have a partner, just find another. And if you can’t, take one by force.” It is 100%, so have a healthy meal ^{_^}