Mane 6 as Mega Man X antagonists (sans Sigma because Sigma would be too easy to include)
Fluttershy - Iris (The hardest one since hardly any antagonist fits Fluttershy at all. However, Iris is a rather peaceful and love driven reploid and both of them are prone to get extremely pained by the things she loves to drift appart like Celestia’s garden animals, getting sometimes the worst of her.)
Applejack - Colonel (Colonel is rather affable at his core and very dutiful to their own, kinda the repliforce and the apple clan. Yet they’re also extremely stubborn and would often get into hot waters out of their inflexibility at their inner codes.)
Pinkie Pie - Dynamo (Dynamo often seems to lack any sense of seriousness or care about the world. Easily the least inclined to conflict if only because he’s not precisely very driven beyond accepting contracts that amuse him. Pinkie and Dynamo often tend to be laid back if also rather unaware of the damage they cause)
Rainbow Dash - Vile (At her worst, Dash is often extremely impulsive, somewhat reckless and is extremely prone to shoot first ask questions later, even if Vile is much worse and far too sociopathic. Both of them love a good fight perhaps a bit too much and could be surprisingly resourceful despite their otherwise brawny behavior)
Rarity - Berkana (Berkana wants to prove she’s the best reploid out of sheer vanity, likes to wear a fairly stylish outfit with a mix between witch and queen. She gets somewhat flirty at X as well during the battle although is often just as dangerous as most of the villains.)
Twilight Sparkle - Gate (A lonely scientist driven mad by their sense of discovery and improvement and constantly feeling isolated from jealous or unsuportive fellows, they are both extremely smart and capable of magical or technological feats above their peers. To a lesser extend, Gate is also the only one of the antagonists from this list who wasn’t a flunky to Sigma but rather directed the plot of the game with Sigma only being a case of an emergency-weapon-resurrection-turned-wrong just like Twilight would rather take the lead over lending the lead to someone else.)