The sixth season premiere follows the show's couples on the second anniversary of Sheldon and Amy's first date, Penny and Leonard's attempt to patch things up after Leonard's blurted proposal, and Wolowitz in space yet caught in an argument between his mother and Bernadette.
The episode felt scattered to me. It had to serve the growing cast, but little time could be spent with each couple in a different setting. Still, I think Raj cut to the heart of Penny and Leonard's problems. Leonard spontaneously yet very plausibly said he loved Penny when they were first dating, to which Penny only replied, "Thank you," freaked out, and broke up with him.
Over the next season and a half, thanks to the growth of the female cast, we saw Penny realize that she missed Leonard and wanted to be with him. The timing of Leonard's proposal would have freaked anyone out, but, more significantly, Penny has yet to say she loves Leonard even though history strongly suggests she does.
TV usually makes too much of characters saying they love each other, but in Big Bang's case, after five-plus seasons, Penny saying she loves Leonard is a big deal. Penny's feelings for Leonard probably do scare her. Saying she loves Leonard would be acknowledgment and acceptance of those feelings, and would mean more than all their breakups and make-ups could mean on their own.