AppleID, MobileMe, iCloud, iTunes mess

Question

Can apple fix the appleID mess it's created?
I suspect almost everyone has this problem.
iTunes was created first.  When you set up a new iTunes account, it creates an appleid using the email address provided.  So far, so good.
Then came MobileMe.  Create a new MobileMe account and a new appleid was created.  You had to use the MobileMe provided [email protected] email address.  This was the default so you couldn't use the same email that you used when creating your iTunes account.  Now you have two appleid's and two different emails, one for each appleid.
Now comes iCloud.  Fortunately, Apple seems to have migrated from MobileMe to iCould without creating yet another appleid.  That's an improvement.  Now, everyone has two appleids, but at least it's not three.
Heres the problem.  When you try to set up iMessage on your iPhone, iPad or iPod you are most likely going to have a problem. 
An email adddress can only be associated with one appleid.  It's a hard one-to-one relationship in the apple database.  Should I use my itunes appleid or my icloud appleid?  What's a person to do?  Ah, the humanity!
If you have associated any email addresses with either of your appleids, then there are going to be more conflicts and you won't have visibility to them.
Here's and example.
Assume iTunes account uses email #1, most likely NOT @me.com because me.com didn't exist when you set up iTunes.
Assume iCloud account uses email #2, most likely an @me.com because that was required with MobileMe.
Assume you have a personal or work address, email #3 let's call it @yahoo.com.  This could also be a work domain, @yahoo.com email or @gmail.com email.
Assume you assigned email #3 to one of your appleid's as an alternative email address.  You probably did this because it's obvious on the applieid form and it's a good idea to have an alternative email for accounts like iTunes, MobileMe and iTunes because they ding your credit card.
Let's say you want your friends to iMessage you at [email protected].  You want this because you want your friends to reach you at email address #3.  You also don't want to give out an email address that is associated with a paid, credit card account, like iTunes and iCloud. So, you login to iMessage with appleid #1.  Then you add email #3, your personal email that you share with your friends.  You want your friends to use your personal, email #3.
iMessage barks, "You can't use this email because it's already being used." 
It would be nice if iMessage would tell you a like more.  Like, which appleid is in play.  Or what you need to do to resolve this.  Or where you need to go.  Sadly, this is not the case.  iMessage would have been equally as helpful by saying, "You're an idiot.  You're not smart enough to use iMessage."
Of course, no one logs into appleid.apple.com regularly.  I completely forgot that appleid.apple.com exists. The UI's for customers are iTunes, MobileMe and now iCloud.
To resolve this, you need to do the following.
1. Remember that appleid.apple.com is the place to go to manage applieid.  I don't have space in my brain for this since I never use it and these accounts are actually created on iTunes, MobileMe and iCould, not on appleid.apple.com.
2. Login into both applieid accounts and look at the emails associated with each.
3. Think about how you want to fix this.
4. Think about which applieid you want to use for iMessage, your iTunes one or your iCloud one.
5. Wonder about the implications of #4.  If I use iCloud for iMessage, can I still buy things in iTunes with my other apple id?  If I use iTunes, will my iMessages get to me?  Does iMessage need the iCloud apple id?  How the heck did I get two appleid's anyway?
6. Develop a plan for moving your email addresses around between both appleid's to resolve any conflicts with iMessage.  You must consider which email you want to give to friends and which you want to keep "secret" for security reasons.
7. Make the changes by removed emails, adding emails, re-verifiying emails, etc.
8. Make changes to iMessage, on every device.  For me, this is four devices - iphone 3gs, iphone 4, ipad 1, ipad 2.
9. Test and hopefully it works now.
In my case, I figured it out and got everything working after a few failures.
I'm not the smartest guy in the world, but I am a tech entrepreneur and I'm a long time user of all apple products.  This mess stumped me for a while.  I can't imagine new apple users my wife or my parents have a chance in **** in figuring this out on their own.
How many calls are coming into Apple Care about this issue?
"iMessage doesn't work!"
"iMessage rejected me!"
"iMessage hates my email address!"
"iMessage is forcing me to give out my secure iTunes email to all my friends!"
Hey Apple, I recommend you take a hard look at the appleID message process as it relates to id and email address management. 
Create a universal appleid for God's sake.  It will be painful to merge, but much more painful if you don't.  It will be devastating if you continue creating new appleid's for every new product.  Users will run out of email addresses and they will lose their minds trying to connect all your great products that they can't use.
If Steve was still here, someone would be fired.  You can do better than this.
My 2 cents.

Answer 1

Yes, it's 2014 and my Apple ID situation is beyond ridiculous. I have a computer science degree and this has had me stuck for months. THe best I've come up with is a seriously snafu'ed workaround that doesn't always work.
Just got a new iPhone 5S (thank you, Apple, for dropping new 4S to only 8 mg so it's completely unusable) and all my apps won't update, my Apple Id - either the new or the old - are completely unrecognized anywhere. I've added, changed passwords, logged out, deauthorized until I'm blue in the face.
APPLE ARE YOU LISTENING????????????? THis is a complete CLUSTER and you should be ashamed of yourselves. No doubt, Steve is rolling over in his grave. You've completely lost sight of his amazing vision.
Just so you know, I've escalated this to the highest level of Apple support and guess what the guy told me - "I've never heard of this problem". Wth?
On top of all the Apple ID insanity, someone else used my email address and created an Apple ID with it. The tech guys never did figure out how to fix it and their sage advice? Abandon both the Apple ID and email address (which I've had since the year 2000)!!!!!! Seriously????
So let's recap - the Apple ID situation is completely unworkable and Apple software allows two people to create Apple ID's using the same email??? I've written code - this is simple. Are you listening, Apple???? CHECK FOR EXISTING EMAILS...
Well, folks... there you have it. A once great company going straight down the tubes. I'm finding ANYONE but Apple to get my devices from in the future.