Franklin Drake essentially inherited the preexisting argument about Section 31 (see YMMV.Star Trek Deep Space Nine for details). Is he a Necessarily EvilPragmatic Hero with the Federation's best interests at heart, or a vigilante who takes stupid risks and gets Starfleet personnel killed and makes moral compromises for no good reason? In particular the latter camp notes the A Million Is a Statistic treatment of the Starfleet Intelligence and naval forces killed due to his actions over the course of the KDF House of Torg Story Arc, noting that if Section 31 really did have the backing its defenders ascribe to it, it would've been simpler and less costly to just tell Worf what was going on through normal channels.
According to later missions in the game, especially "Surface Tension", the main reason for the Federation-Klingon War is that the Federation is heavily infiltrated by the Undine. However, in the KDF storyline the Undine aren't even mentioned until you get to the "Cloaked Intentions" episode (where the Fedside fiasco on P'Jem gets a throwaway mention while you're decoding some Tal Shiar files). Couple that with the war having actually started when the Klingons decided to return to their conquistador days and started attacking Federation colonies, and the fact that J'mpok had been agitating for war with the Federation since 2387, and one starts to wonder if the Undine infiltration isn't really just a convenient Pretext for War. Even if you accept that the Klingons really were after the Undine in the Federation's ranks (as "Surface Tension" suggested), it's hard to argue that their actions were anything but utterly counterproductive, especially after they pulled the exact same damn stunt as with the Gorn in the lead-up to the Dominion War, were completely wrong that time, and drove the Cardassians right into the hands of the Dominion in the bargain.
Is J'mpok the Big Good, Big Bad, a Big Bad Wannabe, or a Noble Demon? He invaded multiple species, killed Martok in a suspicious duel, and waged war against the Federation that weakened the future Alliance before real enemies came calling. He's also helped numerous weaker species, led the Klingon Empire through the worst crises in its history, and reluctantly gone against his own allies on matters of honor. It seems that he wants to be the Big Bad but is a Pragmatic Villainy engaging figure who knows when there's a bigger threat.
Was Worf siding with the Klingon Empire during the Federation-Klingon War the right decision or not? The fact it is the exact opposite choice to what he did during the invasion of Cardassia over similar justifications (invading because the enemy's leadership was subverted by changelings) is notable. Is it because Worf has a family in the Klingon Empire now or did he believe it was more important to be a moderating influence on the Klingon High Council?
Is Kahless II a General Failure and Clone Degeneration that never should have been put in charge of anything, let alone the Klingon Empire's version of Section 31? Or is he a Messianic Archetype that died in a Heroic Sacrifice? He was a figurehead Emperor that Worf indicated was something of an embarrassment but generally harmless. Yet, it was Kahless II who led to the defeat of the Fek'lhri as well as forged the Shard Sword of Kahless that the player character very likely used for many adventures afterward. He died at the hands of an Iconian but distracted it long enough for the player characters to find out their weakness. Generally, players think of him as an idiot but his actions worked quite well against the Klingons' old enemies.
Is D'Tan a genuine reformer who is doing what he feels is best for his people and honestly wants friendship with both of the remaining Alpha/Beta Quadrant superpowers (the official interpretation), a traitor to the Romulan way of life, or a particularly shrewd manipulator who is Playing Both Sides to improve the Romulans' situation?
Subcommander Rai Sahen, a Romulan Republic Intelligence operative who turns up for a few missions in Delta Rising, has been accused of being a Tal Shiar mole for picking sneakier, more stereotypically Romulan solutions to various diplomatic problems (the big one being "Operation Cooperation Conspiracy", a Genghis Gambit she pulls on the Benthans and Hazari by attacking them with a captured Vaadwaur ship in a False Flag Operation). On the flipside, the same mission has the occasional fan asking for dialogue options to wholeheartedly approve of the mission, especially if they're playing a Romulan (the existing options are three variations of What the Hell, Hero?).
The Kobali/Vaadwaur conflict has basically been turned into Designated Hero (the Kobali) versus Designated Villain (the Vaads). See the relevant entry in its own section below.
The ending of the Iconian War. A diplomatic solution (intended interpretation) or The Bad Guy Wins (see here)? Or even something in between (the Iconians did not get what they wanted when they began the War, while the Alliance achieved its stated primary goal... but only because the Iconians changed their minds at the last minute, they still get no comeuppance whatsoever or even promise to try to atone for what they did before, nor do they lift a finger to stop T'Ket from continuing the war on her own)?
Based on what the Talaxian extras are doing in "Reunion" (sitting around drinking, trading shifts to the point where nobody knows who's supposed to be on duty when, leaving spices lying around all over the place, etc.), jonsills and worffan101 reinterpreted Neelix as the Only Sane Man among a race of slackers (to the extent where he's sincerely trying to be helpful and just isn't very good at it).