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The bosses may seem hard to some but they all have that one weakness that when you find out, the boss becomes extremely easy, for example:

When you finally fight the SA-X, you'll notice that it puts off tons of damage, either by hitting you with a shinespark or by freezing you and firing a super missle, and it seems very hard at first, but there's a certain pattern the SA-X moves by, so you stand on the left side while the SA-X is on the right, you shoot it, it shinesparks horizontally at your direction, so you jump to the right and the SA-X is now on the left side, shoot it again, and it shinesparks horizontally at your direction, so jump to the left, and repeat until it mutates, then at that stage the SA-X mutant jumps at your direction, so move to the area it stood on before jumping and once it lands, you shoot it, and it jumps again, so you keep repeating until it's dead.

the game's overall medium at your first playthrough IMO, but it gets extremely easy in your next ones.