Getting 100% is worth it, you do get a longer ending that sets up the next game. Hard mode and Normal mode are the same.
Omega Pirate is the hardest guy in the game, at least he was for me. There are three things yuo have to do to defeat him:
1) Dont get hit by Omega Pirate
2) Dont get hit by Omega Pirate
This next one is the most important
3)Dont get hit by Omega Pirate
Sounds easy right, well its not so get ready to die a few more times.
He has three attacks.
If you are too close he will reach out and smack the living sh1t out of you. Dont get close, this does tons of damage. If you are mid range away from him he will do his wave quake, just double jump over it. If you are far away he will shoot missiles at you, just dash left or right to avoid them, dont get hit as these do tons of damage.
When he is not shooting he will absorb all your attacks, his hand will have glowing circular rings so you know what he is doing, dont shoot, just wait. You have to take out the four phazon parts of him (two shoulders and two knees). It will take two super missile shots each, so dont even bother. Just use the plazma gun and shoot single shots at him. stay in the mid range area so he just does his quake wave. And just keep plucking away. Take your time so you dont get hit. If you get to close roll up into a ball and boost away. Lay a power bomb if you have one to slow him down. It wont do much damage, but he will stop and hop on one leg like he is hurt.
When you take out the last phazon part of him he will turn invisible and two pirates will pop out. You have some time before Omega Pirate is visible again, so quickly take out the pirates. After they are defeated collect any power ups and put on the x-ray visor. Omega Pirate will be in one of the pools of phazon recharging himself. If you are fast you can hit him twice with a super missile, then he will go to another pool of phazon, hit him twice more. If you are slow you not get all four hits on him. It took me six super missiles, one charged shot and one single missle to defeat him. If you are fast you can defeat him in two rounds, if you are slow it will take 3, if you are really slow, you will probably be dead.
After he recharges you will have to start all over destroying the four phazon parts of him again. Do the same as before. This time there will be 3 pirates attacking you. Pick one and destroy it, then ignore the other two. Target the Omega Pirate as before, and jump around to avoid the other pirates. If you dont defeat the Omega Pirate this round just attack him as normal, ignoring the other pirates. The Omega Pirtates wave attack will kill them for you (just make sure there are no pirates hanging from the wall, shoot them down so they get hit by the wave.
After you destroy all the phazon parts again this time there will be four pirates attacking you. Ignore them all completely. Take out the Omega Pirate with super missiles and this time he sould be defeated. All the other pirates will dissapear when you go to the cut scene.
If you run out of missiles use charged shots or single plazma shots. You can also use a super bomb if you time it right, but on hard mode there isnt enough time. You have to get close lay a regular bomb and then lay a super bomb in mid air. This is very hard, so I wouldnt bother.
After you defeat him, go back and save.
Good luck, this was the hardest battle for me. I was very pleased when I finally defeated him.