The problem with RIM is that you're committed to the stability of RIM's services and connectivity. If it goes down so does everything else. It doesn't matter if you're company runs it's own BES server or not. And this is for the most basic services like raw Internet access. This is also why most ISPs charge extra for RIM... they have to route all BlackBerry user traffic through RIM!
The reason people say Windows Mobile is more reliable isn't because the operating system is better (personally, I think it is - at least from a developer's point of view) or that the email application is easier to use. The reason is because most organizations like to remove a point of failure that is not localized by them. By housing their own mail server, when it breaks they can fix it. If you use RIM and RIM breaks the company is at the mercy of RIM to fix it.
You can get another ISP, you can get a different model of BlackBerry, you can run 50 redundant BES servers... but there is only one RIM.
This is so ironic it's awesome. The big bad Microsoft can do nothing but harm and the anti-Microsoft RIM built on the supreme Java (heh) is the savior from the beast. Yet it's odd, Microsoft isn't the ones filtering the bits or flipping your nibbles.--