It is what I believe to be a common predicament:
Apple ID 1 = email@some.domain.com, iTunes purchases (ID set up many moons ago)
Apple ID 2 = email@me.com (ID set up automatically when mobile.me account created)
Firstly, this presents the existing problem that I cannot use my email@me.com (my preferred email address) for Apple ID 1, so have to keep using a different address for that (or I could switch to buying stuff on Apple ID 2, but then I have to sign out and in with my old ID if I have app updates on my old ID, and all my DRMed stuff is linked to my old ID, so I still have to authorize all my computers with that ID too, hassle hassle hassle).
Then, the upcoming problem is that when iCloud launches, a big factor of it (in my mind, at least) is that it allows you to synch all your apps and music (and TV shows were recently added into the mix) between all your devices. This is great, but all my apps and music and TV shows are linked to Apple ID 1.
OK, so I use Apple ID 1 for iCloud.
BUT, iCloud will also include email, great I have an @me.com email address. Ah, but that has it's own Apple ID, which none of my purchases are linked to.
So, what I wonder is, will I be able to merge/link Apple ID 1 with Apple ID 2, to have my purchases form Apple ID 1, and my existing email address from Apple ID 2? Or will I need an iCloud account for Apple ID 1 (which will presumably get a new @me.com address, but not the one I want) and one for Apple ID 2 (so I can keep my prefered @me.com address)?
Also, I now no longer understand what your predicament is. If you want to use your mobile me address as an Apple ID, you can do that right now. It is an Apple ID. It's an issue for those of us who want to keep their pre-existing Apple ID, and use their mobile.me address with that.