One possibility that could work after a fashion is that:
-The crown would need to prove beyond reasonable doubt that sex had taken place; but
-once that had been demonstrated, it only needed to prove on the balance of probability that it was not consensual
So, in circumstances where something had definitely happened, and which looked and smelt like rape, but where there was not conclusive proof, you would still be looking at a conviction.
I don't know how that would play out in the real world. I've suggested it before on this board, and even on here there wasn't much support for it - most posters felt that it would mean innocent people going to prison, and that that was unacceptable.
The thing is, I can't see how, unless there is some fundamental change to the test, I don't see how the conviction rate will ever significantly change?