* PortingDisaster: Arguable for the console ports. The versions on the Dreamcast, PS2 and GBA didn't even try to give you a sniper controller, which took out a lot of the games' appeal. The Xbox version did try to make 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.
* 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.