* Not being able to ship Minecraft in the Win8 store because it uses Java and Java doesn't (yet?) follow the rules required for the store. Store apps require you to use approved APIs, where as Java, being older, calls all kinds of stuff not allowed by store apps.
* Not being able to provide updates anytime you want as each update requires approval.
* Not being able to give away free copies of paid apps (need codes from MS)
* Not being able to bundle with other apps like the humble bundles as the store provides no way to bundle apps.
* Not being able to resell licenses (not sure if Minecraft supports that. If not they could decide to in the future. But not if they're in the Win8 store)
I'm sure others can list more things you can't do on the W8 store that you can do on an open platform.
None of this has anything to do with being certified. Certification basically verifies a publisher's identity and ensures users can do things like cleanly uninstall your program. For this, you get the have a link to your game or application in the Windows Store. Users can click on the link and download like normal. All the other stuff you said applies (may apply?) when Microsoft is hosting and distributing your app (Metro apps).
* Not being able to ship Minecraft in the Win8 store because it uses Java and Java doesn't (yet?) follow the rules required for the store. Store apps require you to use approved APIs, where as Java, being older, calls all kinds of stuff not allowed by store apps.
* Not being able to provide updates anytime you want as each update requires approval.
* Not being able to give away free copies of paid apps (need codes from MS)
* Not being able to bundle with other apps like the humble bundles as the store provides no way to bundle apps.
* Not being able to resell licenses (not sure if Minecraft supports that. If not they could decide to in the future. But not if they're in the Win8 store)
I'm sure others can list more things you can't do on the W8 store that you can do on an open platform.