Well, you claimed that you had to mouse to the application and double-click when using Spotlight, which isn't true.
Personally I don't see any advantage win Win+r over Spotlight, and I use them both since I have to work on a Windows computer. I find Spotlight more efficient except for Win+r cmd, because cmd is only three letters. With Spotlight I need only four keys (or less) of the app name, where as with Win+r, I often need to type a lengthy command, like notepad, for instance. Each to his own, I guess.
Edit: Using Spotlight to launch applications is NOT using a sledgehammer to tap in a thumb tack. Spotlight is excellent for launching applications and it was designed to be, why would search results in the Application folder be the first priority if not?