Even though Season 2 suffers from a bit of a sophomore slump after the incredibly well paced Season 1, there are still some outstanding episodes that I love.
2x11 The First Step: A somewhat new take on the old fighter ace duel. Thrax gets the best lines out of all the Neo Sapiens, besides Phaeton.
2x17 Under the Skin: This episode was just heartbreaking. They take an obscure extra from the first season who was KIA and actually make us care about her. It really changes how we look at that photo JT always keeps in his cockpit.
2x31 The Price of Courage: The Battle of the Bulge of ExoSquad, as far as I can tell. Shiva goes from being a villainous enemy general to an actual warrior who goes down fighting even though he knows it's futile. Downer of an ending.
2x34 One Small Step: The episode where someone dies.
2x38 Abandon Hope: The penultimate episode of Season 2, but pretty much the finale as far as I'm concerned, because it completely wraps up the Neo Sapien War. The last shot really sums it all up.
As a kid I missed the episode of Under the Skin and always just sorta assumed that photo JT had was of his wife or girlfriend. But after watching that episode, it's just so much more meaningful whenever you see it on his windshield. If it had been just a photo of his wife, it would've been completely ordinary and a throwaway detail. But him choosing to remind himself of the loss of Alice Noretti, someone he didn't even know all that well... just tells you what kind of a man he is.