I think that one of the problems facing open source today is the many variations that you can find that stemmed from a single source. One of the best recent example will be Android.
Android OS, being open-sourced by Google, allows anyone to download the source code and do anything to it, subjected to the open-source licence of course. The problem is that as anyone can modify the source codes to work with any kind of devices, it's perfectly possible for some applications available in the Android store that doesn't work well with all Android phones. After all, you're able to change just about anything within the OS.
I've not taken a look at Android in depth but as I recall from traditional mobile programming, you will need to take note of the phone screen size while coding for applications/games for any mobile device. Android being open-sourced will be able to support just about any screen size of any mobile phone. What if the mobile device has some new chip that provides some unique function? So what does that mean for the developers? How will they optimize their applications/games for the Android phone? In the end, you may have applications/games that only work for specific types of Android phones.
Recently Motorola came out with the Droid, based on the Android OS. Recent reviews have rated it highly but if you look at it from a different perspective, you can see the Android OS being splintered and sooner or later, each mobile carrier will try to take Android and do something completely new to differentiate themselves.
How would this impact the Android AppStore? My guess is that it will be quite big. In fact, I don't really see how Android will allow upgrades of its base OS with this kind of splintering going on. From what I understood from friends, the first version of Android OS cannot be upgraded to the second version. I see the trend continuing.
I guess It's the nature of being open-source.
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