A long long time ago I was contemplating the same comparison for an owner looking to move up from a Cheyenne II (he wanted something larger). I don't remember the specifics, but I remember it basically boiling down to this:

1) Buy the King Air 200
2) If you can't afford the 200 but need the size, buy the Cheyenne III
3) If you hate your pilots, buy the Merlin


In all seriousness, the only reason to not buy the King Air is if you couldn't afford it. Other airplanes might have better numbers in some areas, but there's a reason why the BE20 is always on the short list when people talk about the best airplanes ever built. Easy to fly, easy to find quality maintenance, and easy to find a current and qualified pilot should you need one.