I would say there isn't just one person he misses over everyone else (since Soundwave is here). Each had their uses, but there is a top four.

Chronos (Justice League) was his best friend, and one of the few people he'd have nice intellectual conversations with.

Bakura (Yu-Gi-Oh) was useful in that he had the ability to heal and over time ended up becoming one of his friends. He'd often be the one to play chess and other games with him. And Shocky does like his chess.

Starscream (even though he was here for a while) & Quatre (Gundam Wing) are pretty much the ones he went to when he needed to talk, and the two of them usually helped if he needed emotion help or relationship help. It was nice valuable information.