The Crystal.

I'm here for a while but I'm not really used - The crystal gives life to all, and existance, but it's not known so well and it's not "used."

I'm the best or the worst, depends on your perception - As it gives existance to everything, that means it gives existance to good and evil. Also, while the party has the will to survive (therefore, thinking the crystal is the best,), while Necron states that it's 'the worst' because life can only be perfect without existance, or something like that.

I'm used through the entire game but in a different form - Not quite sure what this could refer to. Again, the crystal gives extistance to all, so it's used throughout the entire game. "different form" could mean that it's not seen until the end of the game, when it's behind Kuja, but I don't know.

without me you lose - Without the crystal, existance could not exist, and therefore, Necron would have his way.