MS is working on a os based puerly on C#, I've seen it on channel 9(msdn). It's in it's infancy, it barely had a small kernel and a couple commands. It will be the future. I used to prefer native apps but with mono you also get cross-platform apps and that's a big plus for me; .net will advance alot in the next years as well as C# as the main .net language. I'd say go for C#.