You could just have Maul more and more nibbled away with each film.

The first film he could lose his lower body.

The second film he could lose his arms so in the third film he is Grievous.

It may be possible to replace Jango with Maul in the Geonosis scenes.

It makes no sense for him to be there as having a direct connection to the Separatists pretty much indicates that both armies are being controlled by the same big bad.

This sets him up as being another possible (but false) identity for Vader.

Sure you would have to film someone else as Maul but he is under heavy makeup and probably has robotic legs.

Were the minor cast changes in the Harry Potter films a serious impediment?