In a number of ways, it goes against the premise of a utopian humanity with a "darker side" of the Trek universe. Trek purists did not particularly care for the premise of "In Pale Moonlight" where Sisko uses underhanded methods to bring the Romulans into the Dominion War. The idea that a group like Section 31 would still exist in an era of a more enlightened human society is also antithetical to Rodenberry's vision of the future.
These storylines, on the other hand, do tackle a major philosophical issue Bashir brought up in "Past Tense." "If something disastrous were to happen to the Federation, do we hold onto our principles." With the exception of the first Borg attack, main characters had rarely dealt with crises threatening the Federation's survival.
These storylines, on the other hand, do tackle a major philosophical issue Bashir brought up in "Past Tense." "If something disastrous were to happen to the Federation, do we hold onto our principles." With the exception of the first Borg attack, main characters had rarely dealt with crises threatening the Federation's survival.