Something I'd find... interesting to say the least would be if the characters that went to the Rocket Base actually died in the explosion. Whoever you send there along with Selphie dies. When Seifer hears about it he redeems himself and joins your party, maybe along with Fujin and Raijin. Now obviously the story would change massively if Rinoa were among the victims, so maybe that would have to be impossible. Could also be a neat bit of foreshadowing for Squall and Rinoa's eventual relationship if it was impossible to swap her out. Through the power of time compression, maybe the victims could fight alongside you one last time in Ultimecia's Castle, and then you say ultimate farewells to them after the final battle.

Maybe it would make the game too grim, but it'd certainly have made it memorable. I like the theme of dealing with loss, particularly unexpected loss.