This guide is structured such that there is as little back tracking as possible while still acquiring all of the upgrades and special items throughout the game. As a consequence of this, it means that you might not have a particular bosses weapon weakness ability for X yet, making the fight a little more difficult than it could be if you did. So while the boss orders may differ from other guides, this guide will still show you:
Additionally, this game has several alternate boss fights in the final stages depending on if you defeated certain enemies during the maverick stages. This guide will show these alternate boss fights and explain the factors that lead to getting the various bosses.