People used to say that Microsoft didn't get it right until version 3.0 (or 3.11 for that matter). I've had a line of thought that goes something like this on the subject (not entirely polished, so please give feedback).
When a new type of hardware and software combination arrives, a firm that offers vertically integrated solutions (i.e. develops both hardware and software) can initially offer smoother integration and a better user experience than firms in a horizontal ecosystem (i.e. different makers of hardware and software) can. In the 90's and early 00's, that advantage seemed to hold until the horizontal ecosystem came up with a version 3.0 of its software.
In our ever more online world, firms have also been able to connect online services to hardware and software combinations. The best example is probably how Apple combines hardware (Mac, iPhone, iPad), software (iTunes, Quicktime, Safari) and services (iTunes Music Store, App Store) to create a better overall experience.
Another example is how Research In Motion has combined the Blackberry phones with the BBM chat service to create something special that competitors don't offer. One of Nokia's issues seem to be the inability to create a hardware, software and services combination that can compete with the iPhone.
It might be even harder for a horizontal ecosystem to replicate the ease-of-use of a vertically integrated system when it also needs to get the online services right (see Android Market). Especially as major players in the different layers don't fully trust each other, as they've seen how the majority of profits often flow to a few firms (an example being Microsoft and Intel in the PC ecosystem) and few firms want to "take on for the team" to make sure the ecosystem grows strong.