You already seem to be aware of the short answer, but I'll reiterate it here for clarity:
Win32: Powerful and complete. Any documented behavior on the windows platform can be composed via Win32, but with power comes responsibility and difficulty. There's a pretty significant amount of subtlety and difficulty in creating rich Win32 experiences.
.Net: Powerful, but a subset of Win32. .Net provides more than enough capability for the vast majority of line-of-business apps and more, but rich UI and specific, specialized situations simply don't exist within it because the BCL, for whatever reason, doesn't believe it makes sense to support it. The most common example that I've run across is UI capabilities in newer versions of Windows, though there are other areas where PInvoke is useful. .Net is a much simpler model to grasp and work within, however, and (in my experience) the subtlety of .net is much less likely to shoot me in the foot than Win32 is.
If you include dllimport and PInvoke, then I'd guess that .Net is a reasonable alternative that's capable of performing suitably well in 90+% of tasks, and WPF brings a whole different level of rich UI to the managed world.
