These are all from my POV. Your mileage may vary.
Advantages of .NET:
- Cross platform capability (via Mono and .Net Core)
- Good selection of framework classes typically means less code.
- Easy integration of components, regardless of the language the component was coded in. (You like F#, or IronPython, great! Code your assemblies in whichever language is most appropriate.)
Disadvantages of .NET:
- .NET means different things to different people. (For example where does WPF come into the equation?)
- Sometimes DLLImport and/or PInvoke is the only way to get to the functionality you need, which means you lose the cross-platform capability.
Advantages of WIN32:
- If you know what you are doing, you can construct great applications with minimal dependencies.
- More suitable for "low level" operations than a .NET based solution.
Disadvantages of WIN32:
- If you don't know what you're doing, you can easily shoot yourself in the foot in a more application or system fatal manner.
- You frequently have to write code that you would get "for free" using .NET.
Both have their place, and will probably continue to exist until a true replacement OS (Midori? Some form of web-based OS?) comes online and gains widespread acceptance.
