The thing is, other than these books (Vanguard, Errand series and Cloak), I'm not that familiar with "darker"/"sophisticated" TOS novels, and would love some more recommendations..
I suppose it depends on what sort of thing you're looking for. Errand of Vengeance
has the connections to Vanguard
, and Cloak
has the kind of dark overtones that you would associate with Section 31.
I take it you're after something that goes beyond the "planet-of-the-week" formula, but I don't know if you wanted to delve into politics and intrigue or have more character-driven stories.