* MoralEventHorizon: The BigBad in the second game, ''Dark Silhouette'', crosses it when he places launch devices of the missiles onto three hostages in the opera to guarantee that the missiles will launch and so that Falcon and Jackal won't be able to prevent it.
* PortingDisaster: Arguable for the console ports. While they are solid from a technical standpoint, the versions on the Dreamcast, PS2 and GBA didn't even try to give you a sniper controller, or any form of light gun support at all for that matter, which took out a lot of the games' appeal. The Xbox version did have light gun support, and some editions even came bundled a sniper rifle accessory, but the scope didn't really work and it was very unwieldy and cheap-feeling.
* ThatOneBoss: Cobra, in the first two games. In the first game, he's either running with the president's daughter on his shoulder, or riding in an erratically-moving car while using her as a {{human shield}}, and ramming you with a semi truck after that. In the second game, he once again uses a human shield while on a moving vehicle, and he also throws alot of stuff, including hostages, at you.
** Monica in the original. She wears armor, has 10 HitPoints (instead of 5 for previous bosses), hides a lot, [[MostAnnoyingSound taunts you repeatedly]], and uses the President as a human shield.
** The penultimate boss of ''EX'', Phantom, drives a hover tank with an InvisibilityCloak, is hard to hit, and [[RammingAlwaysWorks attacks by ramming]].
** Almost every boss in the console-only ''SS 3'' is this, due to the lack of a light gun peripheral and the clumsy controls. It's rather telling that Cobra makes a return from the first two games as the first boss of the third.
*** Shaker, the boss of the casino stage, makes those aforementioned problems worse via use of his giant roulette wheel, which also has hostages and some of his goons riding it; Shaker becomes somewhat easier once you take out all the goons, as he himself doesn't attack at all. Still, it's hell to get a headshot on him. He does let out a rather amusing [[BigOMG "Oh my god!"]] once you take him down, though.
* ThatOneLevel: All three penultimate stages in ''EX'' are just horrendous no matter which one you pick. Take your pick between:
** A StealthBasedMission where one missed shot or instance of taking too long results in mission failure.
** A hang-gliding stage where you have to snipe enemies in a moving hang glider. It will end in failure if you don't clear the landing platform of enemies.
** An underwater stage that is not only on a time limit, but this being underwater, your shots move much more slowly and are easily affected by currents that are not always obvious to see.