I don't think a strait natural finish would look that good with the number of body pieces and the different wood colours - there's a reason Fender used alder for solid coloured guitars and ash for the sunbursts and clears.
If you are staining it, then I think you'd need something quite dark to tie it all together. If you were spraying, then you could try a butterscotch finish with a black scratchplate. The semi-opaque light-cream base coat would hide most of the join lines whilst letting some of the grain patterns through.