Looking at Kensuke, he seems to want to say, "I don't have a mother… How pitiful I am."
Shinji:“You'd better not. Your mother would be worried.”
Mr. Tines: For the first time this episode, some genuine eye-contact by Ikari-kun.
Incisivis: Shinji's attitude towards Kensuke's war games is one of distance and slight confusion. He says that Kensuke's mother might be worried if he piloted an Evangelion, and can't seem to grasp that Kensuke would do these things for fun (hence the "guerilla warfare" question, which I think is willfull ignorance). This happens because at this point in the story Shinji is basically pacifistic. He's had hatred and now violence, but his surface self still dislikes them. It illustrates Shinji's lack of masculinity, but also that it's hard to romanticize something once you've experienced it firsthand.