I'm not familiar with the RPGOne, but in all honesty I enjoy the GBA version as its more eloquent and fleshes out the characters personalities better. Kefka seems downright more evil in the first half of the game instead of the comic relief sidekick villain that Ted Woolsey script portrayed him as. Character like Setzer and Sabin are given a better sesnse of depth to them through their dialogue. From a story standpoint the GBA script just improves everything.

Seriously, after finishing the GBA version I could honestly say VI has the best written and overall best story in the series. Before I played the game I would have said it was the best for its time... Granted I don't think it will win anyone over who didn't like the game to begin with; but if you loved the story, its nice to see it fleshed out a bit and written in a more mature fashion.