I thought Windows already supported cryptographically signed programs, isn't that how it identifies who the publisher of a piece of software is when it asks if you're sure you want to open it? All it lacks is a means of denying unsigned apps similar to OS X's Gatekeeper.
However, what I would really like to see; on Mac OS X as well, is a setup wizard that actually guides users towards a secure setup. On Mac it's still a good idea to have a separate administrator account, and on Windows the same applies, as even if a UAC bypass is discovered it still can't do anything if you only have a standard account for the majority of your software.
On Mac, this setup works well as it will just prompt you for an admin username and password, so you can still do stuff using your admin user's permissions, without having to sign in as them, but I'm not sure if Windows supports this at present?
But yeah; while the majority of systems are probably single-user, Windows could really do with asking users to provide two sets of passwords or other credentials, one for the admin and one for general use, so they can get the convenience of a simple password for common operations, but a more complex one for secure operations.
There's definitely an argument for how an OS should treat security; endless prompts are a bad design decision as it trains the user to dismiss them as an inconvenience, but really what a good OS should do is train the user to act in a more secure way, and recognise when something shouldn't be asking for permissions that it doesn't need.