The ideal prequal for me would deal with what would concievably be a good first team of x-men: Cyclops, Jean, Havok, Avalanche, Wolfsbane, and Beast (prefur, like in X2) and the origins of the X-Men. It would be awesome to have it be more cyclops oriented and to focus more on their character developement. I don't know if the Magneto movie is gonna show Magneto's split with the X-Men but ideally no. Basically, my idea is that the movie begins with a flashback to the plain crash that killed scott's parents and gave him brain damage making him unable to control his powers. The main story could revolve around the x-men meeting each other and learning how to use their powers under Xavier and Magneto. They end up infiltrating Genosha in an effort to investigate the mutate process and exploitation of mutants. They end up prisoners in a concentration camp where cyclops meets storm (explaining her anger and accent in the first movie). Beast is subjected to experiments which will eventually alter his physical appearance and Wolfsbane and Avalanche are killed. Havok is so traumatized he leaves the team and the incident disturbs magneto so much that he leaves the x-men with a young Genoshan inmate named mystique. The main villain could be Commander Cameron Hodge and heck, he could use the blob and Unus the untouchable as his enslaved lackeys.
There's a good fourth x-men film. It's a prequal, it stays on theme, it uses characters in creative ways without bogging them down in comic cannon, and it fleshes out characters other than Wolverine