I think the system as it sits is probably the most productive working relationship. Anyone who cares to can develop a technology, submit it to become a standard, and then Microsoft and Apple implement that standard in accordance with the market's wishes.
We've all got our complaints about one flavor of OS or another, but the reality is the work we do with these machines is where the similarity begins and ends. What tools we prefer, and how we choose to do our work, will always allow for variety.
That said, if you make things work together too easily, you lose competitive advantage and potential revenue. Why would you willingly standardize your mobile devices on USB connectors, thereby losing all the revenue from cables and accessories?