The battle had me thrown off a little, but other than that, I found it enjoyable.
I wonder though, why did you recolor Magus?
Aside, the plot twists were awesome, but my only concern is the end scene. If the characters had previously defeated Lavos, why didn't the future change as well? Wouldn't it be more hospitable? And shouldn't Crono and Lucca have known where they were, since 2300 AD was a place in time you could travel to in the game?
And a comment at Fissile,
No matter what period (12000 BC, 600 AD, 1000 AD or 1999 AD) you fight Lavos, it remains dead all the same since you appear in some sort of time vortex for the battle.