I think we should remember that MS and Apple are selling a different products. MS are selling a platform for OEMs to build their mobile "Smart-phone" on top of their platform as a base layer, while Apple are selling a phone to end-users - the regular consumers, without trying to offer it as a solution to OEMs.
To continue selling the Windows Mobile platform to OEM companies MS have to keep the platform flexibility and allow OEMs to implement this level of customization with their devices and probably even more. If all Windows Mobile devices will be the same and will be shipped with the exact similar content then there isn't any need for such competition model between the different OEMs as they will all be forced to ship the exact same phone.
MS business model in this case is structured on the fact that they generate a complete market relying on their platform of different OEM companies that also compete between them on different implementation of MS OS - just think about the great position that such structure puts MS in!
I doubt it if the third-party applications market actually include more than 5% or so of all of Windows Mobile users since most of WM users simply buy a device to use the built in features that arrive with the device. This means that when HTC adds a new weather solution with their device they are offering a completely new feature that other companies doesn't have on their device (with the understanding that most users aren't familiar with the existence of third-party application option for their mobile device or they simply won't know how to install it).
Since I believe the third party applications market is relatively small from the large MS eyes, I don't think that the fact that there are lots of different variations for Windows Mobile devices is effecting MS too much, nor the majority of the Windows Mobile users.
Due to the difference in the models and target market between MS and Apple I don't think that we will see any changes soon since both companies simply have a different path in their hand and the only question is simply when one of MS OEMs will be able to produce something that will run on WM that will offer a better mobile solution from what Apple are offering at this stage.
Cheers!
