Hmm, the definitions are in \Data\Scripts\include\PilotProperties.script, you mean, not "pilotdefinitions.script"? couldn't find that.

I understand what you mean about the UI. \Data\TEXTURE\Interface\Pilot\PerkTree\ pretty much tells me each pilot has to have their own graphic, and the .ini file to show which perk slot goes where.

But this doesn't tell us the prerequisites perks, right? E.g. to learn skill X, skill Y must be learned first <-- where is this determined?
Edit:
Hmm, is it those ugly properties_<pilot name> = { ... } structures inside PilotProperties.script? That does look likely but I don't understand the { numbers } stuff. Wait, I think I got it... the number is the perk's cost in exp points, then anything following that in the nested {} are the prerequisites. Ok, I think I understand.