Roy's resolution in Shamballah is better than FMAB's ending for Roy. Cursed with the memories and grief of his war crimes, he commits a sort of intellectual suicide by sequestering himself in a remote snowy region as an outpost guard. (A huge step down from Brigadier General). Even his revenge against Bradley for Hughes death was done out of a sense of honor and guilt rather than genocidal fury against Envy.

While Bradley's death had more showmanship and climactic presentation in FMAB, the 2003 version is much more satisfying and vindicating of Roy and the general themes of that show with Bradley's death in that version.

The State (called Amestris in FMAB) is also dissolved from the military dictatorship under Bradley and back into a parliamentary democracy.

I didn't like the presentation that FMAB Roy's aspiration of becoming a compassionate Fuhrer as a way of resolving Amestris's issues and prefer the systemic rehabilitation of the state and nation in the 2003 version.

They're both equally good but despite having the same name and story - up to a certain point - they're completely different the way apple cider is to water with an apple slice in it is.