Security disaster in the making
As Steve Davies mentioned, there will be security vulnerabilities found in the .NET libraries; it's a question of when, not if. The real problem is what to do about them, now that the libraries are bundled with apps.
On the one hand, they could let developers release new versions of their apps every time the libraries are updated. Realistically, most of them won't bother, which creates a large attack vector. I'm sure VXers will find a way to take advantage of it, such as convincing users to install vulnerable apps which can be exploited. (E.g., "you need XX video player to watch this clip of [celebrity]".) Will antivirus programs have to start flagging anything with outdated libraries as potentially harmful? This way lies madness.
The alternative is to push security patches through Windows Update. Except this is supposed to be cross-platform, so you don't necessarily have Windows Update. Maybe solvable with an updater service, but now that also has to be bundled with apps as well, and could lead to issues with multiple instances and version incompatibility if you install several .NET apps. Even with that solved, pushing updates could break signed apps.
Anyone have better ideas on how to not have this turn into a nightmare?