This has been bugging me, thinking about the implications of the final showdown in FMA. Since I can't really avoid spoilers (duh), it's all behind a cut ( ...shorter version: wherein there's question of reset buttons. )
Maybe there weren't a lot of gaps in the course of the overall FMA storyline... but I can sure see a whole lotta possibilities for fanfic when it comes to grappling with the consequences of questions Arakawa left unanswered.