As far as things go, I don't think Apache OR IIS is a simple system to work with. There's strong and weak points to using both of them. I think I'd rather have Apache overall, but I'm not a web guy and to me the products are pretty close in terms of functionality.
Godaddy is probably switching because they've been offered some unbelievably sweet deal on MS licensing and a ton of sales support. Microsoft gets a big, recognizable feather in its cap for its work.