I honestly think I have no opinion on this. I can't really say I "ship" Shinichi with anybody - not even Ran, really, though to a point I want to see them end up together, but I'm not gonna lose sleep over it if she dies or anything. To me, it's more about the cases and Black Organization plot.
That said, if both Ran and Shiho died, and Kaitou KID disappeared (--I would just like to pause for a second and wonder about this. Apparently I'm not deep enough in to the 'fandom' side of Detective Conan, because I had no idea that ShinichixKaitou KID was big enough to warrant making him disappear for the sake of variety--), I think the one that I would most likely want to see happen would be ShinichixVermouth, but even then, I'm not solid enough on that to vote for it.
I will say, however, that I would NOT vote for Ayumi, Kogoro, Eri, Yukiko, Yusaku, Megure or Agasa. Or Sonoko.