The Hunter is generally slow so as long as you are patient your attacks, his attacks could be easily dodged (evade/jump).
Run and Charge:
The Hunter will jump off to a distance first, then run and charge towards you. Immediately he'll make a U-turn and repeat the same motion another two times. You can shoot while you wait for him to charge towards you, and evade to the side before he hits you.
Boomerang in the dark:
At some point the Hunter will hide itself in the dark and throw a spinning knife (that looks like a boomerang) at you. It cannot be countered but is easily evadable. You don't even have to move/dodge. Just stay on the spot and double jump in time.
If you can kill him fast enough (not possible for first playthrough), you can skip this phase altogether.
Hand out of the ground:
The Hunter will shoot something at the ground creating a giant 'hand'. The game teaches you how to evade this the first time it occurs in mission 1, but screw that! Why evade when you can counter for free?? As soon as you see the 'hand' rise from the ground, press /\ and you'll return it right to the Hunter for good damage.
Last updated: 16 Feb 2013