It’s easy to determine if targeting is on the .NET platform, and if not, tell users where to download them. I am not a fan of reinstalling the bootstrap installer; something a hacker will do. Let the user get it directly from the source.
Vista comes with 3.5. XP SP2 comes with 2.0 XP SP2 is required for .NET 2.0, but .NET is never installed by default for XP systems; its always optional. This is almost the minimum specification for any MS desktop system; if they are running XP sp1 or earlier, I would avoid them unless you have specific requirements (embedded systems, dumb / stubborn user base, etc.).
edit: I could have sworn that SP2 came with .NET 2.0, but I can’t find the final information about this.