Ledo saying, "Thank you," to Amy at the end of episode three. Deep, considering these are the first words he said in her language (and especially cute how he stumbles over the foreign syllables).
The party in episode 5 was apparently Pinion's attempt to cheer Ledo up for not finding a job. It also explains his annoyance at everyone else crashing the party—he just wanted a little, private affair for Ledo and his close-ish friends.
Amy's private dance for Ledo in Episode 6 was both sensual and tender, especially with the music and the "ocean auroras."
In the latter half of the series, Ledo's struggles with the moral implications of his position and his life show how hard he's working to overcome his own ignorance and an entire life of ingrained obedience in the pursuit of doing the right thing. Highlights include refusing to kill the Hideauze once he learns that they had a close relationship with humanity and attacking his highly respected superior officer to save his friends and their people.
Ledo: (as Chamber ejects the cockpit) What are you doing?! Chamber!
Chamber: I am a Pilot Support Enlightenment System. By helping you achieve results, I fulfill my purpose of existence... All of this sea and sky will surely give you possibilities. Survive. Explore. I expect great things from you.
Striker: A Pilot Support Enlightenment System does not have the authority to reject a pilot.
Chamber: He needs no support. There is no more room for enlightenment. Now, after I eliminate the barrier that blocks his path ahead, my mission will be complete.