[professor_scissors]

The story is standard Kojima faire, and is thusly interesting but forgettable.

As for Fighting Some Dudes 101:
Dash alot. Rapidly tapping R2 is faster than holding it. Dash Attacks are very powerful and hard for your enemies to avoid. If you're righting the normal flying mechs, a good solid strategy is dash+square, square, square, square, dash away, repeat. Generally avoid using the homing laser as anything other than a way to irritate enemies who aren't close to you, as its damage is not very impressive.
Against Mummyheads, use O to grab and throw them at other enemies/walls. A fantastic skill, as it destroys their barrier, turning them into normal enemies.

Any particular encounters giving you trouble?

[professor_scissors]

The thought of next-gen Zone of the Enders is breathtaking.