Foe Yay Leviathan and Bahamut, although it's mostly from Leviathan's side. Especially evident in his between-mission briefings, were it's evident that Bahamut's turning away against the Commonwealth and him, hurt Leviathan very personally.
Game Breaker: Sayuri, Sayuri, Sayuri. She cannot wield guns, but her sword kills all enemies except bosses in one hit. And against bosses she does ridiculous damage. Her Razor Wind charge shot also goes through everything, unlike charged Heated Plasma, thus allowing her to hit many enemies offscreen where other characters can't. Her upgrades in Rising Mode make her even more broken. She can get a speed upgrade to her movement. You can also buy upgrades to her sword that can make her do up to double damage against everything. Since weapon capsules don't do anything to her, she's always at full power and not subject to Continuing Is Painful like all other characters are. And the final nail in the coffin? You can buy automatic fire for her, meaning that you can just stand there and hold the X/Square button to hack away at enemies, and while you're doing so, charge up her charge shot which you can shoot off whenever you need to by briefly releasing the button.
Harsher in Hindsight: Bahamut's killing of Mandrake in one of the endings in the original Contra Hard Corps comes off worse as Uprising shows they've been allies for years.