I was thinking this over and the only character we see wearing a Starfleet Command 'starburst' insignia and in command of a starship (in any capacity outside of Stocker's emergency command) is Wesley. We have Komack who is the apparent commander of Starfleet then Stone, Mendez and Stocker are all starbase commanders.
I still think that Wesley was involved from Starfleet's end with the development of the M-5 and was commanding the task force in that capacity. I don't think there's any evidence that he is the regular CO of the Lexington. He's apparently excited about it at the beginning of the episode and would be an easy explanation as to why he is the Governor of Mantillies (M-5's failure).
Interesting side note: Commodore Decker's insignia doesn't have a command symbol on it.