First, I would make you level up A LOT faster after level 40. No more 129 hours of fighting Iron Gigants just to get to level 97.

Then, I would add Ultima Weapon to the game...

Once you've beaten Shinryuu and Omega, an extra dungeon would appear where you fight monsters that are about as tough as Neo X-Death and several bosses that are about as tough as Omega or Shinryuu. And there would also be some cool weapons and armours in the dungeon, of course. And then... in the end of the Dungeon, you would have to battle Ultima Weapon!

Ultima Weapon would NOT have his HP limmited to 60,000... because he would have atleast 1,000,000 HP. His attacks would be pretty much a mix of Omega's and Shinryuu's attacks... except the weak ones.