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These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Game Breaker: The Slave ship, with its tiny hitbox and incredible firepower, is the ship of choice for the high score leaderboards everywhere.
Some consider the Judge Spear itself to be a Game Breaker. Fully power it up and give it a Slave formation that makes up for its lack of defensive spread, and you can easily tear through large enemies (and earn QUICK SHOT! bonuses that most other ships would find impossible to earn) and bring down bosses in very little time.
Better yet, Judge Spear Slave, so that the Slave with its high damage and and small hitbox inherits the Judge Spear's ridiculously powerful bomb and fast movement speed.
Good Bad Bugs: The Fairy in the second entry is still able to graze and fire while firing her flamethrower bomb. Some players exploit this for extra points or take advantage of the long invincibility time. This got nerfed with reduced power and duration in Jet, naturally.
That One Boss: Jet has several. Red Eye, the final boss of the second game, reappears as the final boss of the neutral stage path, and difficult as it was in the second game. Most notorious is the first boss of Phase 2, which is a giant tank that moves extremely fast, floods the screen with very slow bullets, and fires off almost undodgeable bullet spam if you destroy its forms at the wrong time.
Tier-Induced Scrappy: Raiden mk-II and Raiden mk-II Beta. The former is more infuriating by being slower than in the Raiden series. The Beta is faster, but has a very crappy Bomb and no rapid-firing capabilities.
The Endeavor in the first game fits this trope to a T. Sure it has an instant-charge Laser special and the only subweapon that can absorb enemy fire, but its main gun has a very low rate of fire and its Laser weapon does not cover the front of the craft.
On that last note, however, it should be noted that it allows the player to avoid enemies that project heavy firepower to their direct rear (and there are quite a few of them that do so).
The developers probably realized how much the Endeavor was reviled in general that, in a cameo appearance in Raiden Fighters 2, enemy tanks refused to run over a bunch of them sitting on an airstrip.