if you only like jay throughout a SOLE specific stage (*cough* "rogue" *cough*) then you're not actually a jay fan and that's okay but don't pretend like you are
IMO his arc should have been about accepting that's okay if he's not the same as pre merge. Jay can love, be loved by the team, be a full person and become a ninja again but better and with more experience EVEN without memories
I hope that at the very least Jay in P2 remains as smart as he was in s3, the way he did an elaborate plan that no one believed in, how he saw a cool mech and decided to hack it knowing it would be useful later, the weapons he used in p1, how he figured out about the fake graves