"8. McCoy claims Kirk is not well after the attack on Starfleet Headquarters, scans him on the shuttle up to the Enterprise, and he seems to be a lot more winded/injured on "Kronos" than would result from the fight with the Klingons - but this is all forgotten about and never mentioned again."
I must agree on this point. I whole hardheartedly expected for Kirk to be under some kind of control and when section 31 became involved in the story I thought that a plot would emerge from that. It did not.
That being said can't we all get just back on the Carol Marcus underwear scene again?