Shego didn't respond to the first comment because she wasn't the one all messed up with mommy issues and she didn't consider her (almost nonexistent) relationship with her mother to be even remotely relevant to why she was on the Barge.

"You've seen how the network's all screwed up, right? He's talking to his buddies from back home. Maybe had to go remind Sylar that he's a jerk, too. It's not like we're married."