When I started this fic, it was indeed based on Melee. Now that Brawl is out, does this mean I'm gonna try to play catch-up and start plugging in Brawl characters? Does this mean that I'm gonna throw out the ending I originally had intended and create one that ties into Brawl?
Not at all.
Yeah, we all know Brawl happens eventually, but this story was never meant to lead into Brawl and it probably never will. I started this in 2004; way before I (or even Sakurai himself) had any idea for the next Smash Bros. The ending I had in mind definitely has changed over the years, but none of them involve Subspace or another tournament. The sequel would pick up wherever I left off here.
And, of course, like Kr3wman said, it's Fanfiction. This can go in any direction, and it has, from having Mario and Link face off against Cloud and Squall to throwing them into a hellhole from Chrono Cross called the Darkness of Time (which should actually be called the Darkness Beyond Time. D***it...).