You'd think that with such a massive, decades-spanning franchise of franchises, there would be more good fanfiction! But nope, almost all of the fanfiction out there is written by icky fangirls. Gundam has enormous potential for good fanfiction, so hopefully more of it emerges in the coming years. Many of the sub-franchises feature huge, well-developed worlds that are full of potential for the telling of new, divergent stories.
That being said, there are a few fanfics out there worth looking into.
Mobile Suit Gundam Iron Blooded OrphansThe Devil's Reprisal by Diablo Snowblind
- Recommended by JSRGN
- Synopsis: A time travel story of Mikazuki Augus returning to the beginning after the final battle. Decidedly Peggy Sue.
- Comments: The author just started it, but this story already looks like something special. There's a lot of background development, a dark tone, and a unique Tranquil Fury portrayal of Ace Pilot Mikazuki. The story is extremely well written, and the author doesn't look like he's going to bother sticking to the stations of canon.
- Secondary comments: The worldbuilding is top notch. A possible contender for the overall best Gundam fanfic.