1. Change the behaviour of Mac OS X to match Windows in terms of Window Minimizing, access to desktop, file sorting and so on. Simply, make the transition a lot more painlessYou're not a Mac user, are you? Because Apple's popular because it's uncompromising in its features. The things you named, though... are the same. You minimize things the same in both. You access the desktop the same in both. You sort files using very similar systems, though each has its own flaws.
2. License out Mac OS X for specially designated high end machines by big vendors. For example, make a VAIO version of Mac OS X that works only with those laptop
Apple already does that - with Apple computers. It's what lets them integrate themselves so tightly. So, now they're going off to Vaio to do... what now?
3. Expand the Apple App store to also become an OS X App store.
http://apple.com/downloads not good enough for you?
4. Add a feature to the iPod and iPhone that only works with Mac OS X. For example, some type of 3D file manager that 'requires' OS X to work
So you're asking them to cripple popular software? Because that hurts sales for their best-selling products. That, in turn, will probably hurt Mac sales, due to damaged reputation. A lot of people get iPods then get Macs because the experience is so enjoyable.
5. Offer some type of open source framework that allows virtualisation across platforms like the iPhone, Web and other OSes
"Virtualization?" Christ, MobileMe already syncs everything. And the iPhone already runs OS X. What more can they do? (I'm genuinely curious what you mean on this one.)