Any intelligence officer worth his classified salt would have had our ships disguised as generic freighters rather than anything that would have immediately called attention to us, much less military vessels in the service of one of the great houses.
Though given how Drake's been going around introducing himself and blabbing on and on about Section 31 to every Starfleet captain in the quadrant, it would seem that the organization has really taken a downward spiral since Sloan's day.
Yeah. I generally hate S31 in concept, but they've gotten just plain stupid in STO.
I think most of the time travel missions focusing on the Original Series era is a tip of the hat to the fact that most Star Trek games are set in that time frame. There are quite a few diehard fans whom cryptic was trying to cater to. I am not entirely sure how I feel about that.
As for Fraklin Drake, yes he did do a **** poor job on the cover story. His appearance in the enitre STO story line is a little messed up starting with his "attempted" defection to the Romulans.
I would like to se him added to the background of the Tutorial mission, by offering obscure information either on the Khitomer, or at the Vega Colony (possibly foreshadowing events that have [or have yet] come). Putting him on ESD or at the Celes System Starbase could further add to the slow introduction to the character before the shocking events during the Romulan front mission.
My final thoughts on Drake is that I hope he eventually gets played by the Iconians, then assimilated by the Borg so that we can put him down like the dog that he is.