Easy Metals:
This trick requires a Life Tank, but it does not have to be full. Spend all your Metals until you have less than 50. After that, buy the Life Charge Chip. Normally you cannot buy it if you do not have more than 50 Metals. If it works, you will see the Metal counter get crazy. You can now buy anything at the R&D Lab. If you take any Metal on a stage, the metal counter will drop to the top (9999999).

Alternate ending sequence
The character that kills Lumine (Axl, X, or Zero) will determine which ending sequence appears.

Axl's White Armor:
Successfully complete the game with all of Axl's metals and use Axl to defeat the final Boss with a double attack.

X's Ultimate Armor:
Successfully complete the game with all of X's metals and all eight armor pieces.

Zero's Black Armor:
Successfully complete the game with all of Zero's metals.

Zero's Sigma-Blade:
Successfully complete the game and load your cleared saved file. You can buy Zero's Sigma-Blade at the R&D Lab.

Defeating Bosses
Just have both character's life at full and perhaps a Life Tank. You can kill every Boss with only the Buster and Saber.

Bonus characters:
Successfully complete the game and load your cleared saved file. The navigator used most to complete the levels will be unlocked (Alia, Layer, or Palette). Alia is similar to X with an X-buster, but cannot use armor pieces. Layer is similar to Zero with a Z-saber. Palette is similar to Axl, but has no DNA-copy abilities