While I know it is a pipe dream, personally one of the things I would love to see out of a higher MP sensor someday would be some more flexible CFAs. A 40MP sensor could easily throw in an IR or UV channel, some other colours, or even throw in some ND pixels and get single-shot HDR which would produce some nice dynamic range.
Sadly, all of those things kinda break from 'just do what you have been doing, but more!'.