I wrote a fanfic many moons ago (mid-90's) that had a very similar setup to Trek 2009. Where the Enterprise-D and another starship were thrown back in time. The other ship arrives first and the Enterprise arrives sometime later to find that the timeline had been altered and Khan had won the Eugenics Wars.
It had a Picard vs. Khan element though I never thought it really worked. I know I have the outline at least packed away in a box somewhere.