It seems very random. When i was on the chitose route (moonlit lovers), chitose naturally had the highest affection but had some negative stats...such as -2 to hit rate. Logically speaking, the higher the affection level, the better the pilot stats right? Does anyone know how pilot stats are determined?

Even characters with similar affection levels can have wildly differing pilot stats.

P.S. Does score (in the after combat screen) do anything?

Stats depend on mood, which is mostly scripted. Affection determines the route split in GA1 and that's it IIRC.

Battle performance affects the debriefing dialogue and maybe mood/affection, score doesn't matter.

Then what does trust do in GA2 and 3? The pink bar under the potrait in the whale room.

I think i figured out how pilot stats work.

Pilot stats are mostly dependant on the potrait color in the whale room.

Base level is green, then it goes up to yellow and pink.

Problem is that this is mostly out of your control, most of the angels will have terrible stats in the second moonlit lovers battle despite having pink mood, because of plot.

Also you don't have enough time to talk to the angels in most cases, so you can't raise their mood, and sometimes you don't get any chances to see their mood before a battle (e.g. the final battle).

From what i can tell it takes 2 positive choices to go from green to yellow, and sometimes you simply don't get enough time to talk to a particular angel twice (e.g. right after the angel wing is assembled in ML, you can only talk to each angel once except the route girl).

But there still seems to be a lot of variance involved, highest pilot stats are right after you make up with your route girl (3rd battle usually), and it's way higher than what you get in other battles even with pink mood.