Well, I got these fics to look at (barring some of my own horrible fics I wrote).

One's Star Wars: Awakening by Dave Gremillion. This is a rewrite of Episode 1, which surprisingly matches with the pre-99 EU and has one thing that most prequel rewrites don't usually have which I can't say because of spoilers.

Another's Project JS by P99. This is also a prequel rewrite, but there's an interesting twist to it: Obi-Wan's a clone of a Jedi Master. I think that's all I need to say. Not really a spoiler because they establish it in the first chapter.

Finally, there's Balance by Xander867, a fanfiction of The Clone Wars cartoon. Here, Ahsoka teams up with a Pureblooded Sith named Adas and they try to deal with the Clone Wars. This is an edited version Xander867's earlier fic Secrets Inside of Me, which is just as interesting, but I feel Balance is better written, the story flows better, and the characterization is more believable.