I know a lot of people have previously asked this question. However my problem still has not been solved. I have iMessage on. I am using iMessage via my Apple ID. Now where it says "receive at:", it shows my email, and it won't even let me remove the email. Plus it doesn't even have an option that shows my phone number. I have an iPhone 4S. I have tried opening iMessage without an Apple ID, however it says "Verifying" for hours and hours.
The only tried and true manner I've found to resolve this is to force Apple's activation servers to see the phone as a new device. The push notification servers have clearly "hung on" to what it thinks is the correct iMessage information despite your efforts to correct this.
To accomplish this, you'll need to be really careful about keeping a good backup since you will have to erase your phone and set it up as new. I recommend making an iCloud backup, then making a local backup to iTunes. If you are really paranoid, back up your PC/Mac at this point and have two copies of the iTunes backup. I would turn odd iMessage and power down the phone and then make a backup once it starts with no iMessage on the phone just in case the iMessage settings could get restored after you perform this erase operation.
Now you will need to be sure your phone receives SMS messages. Your carrier should double check that your account has SMS enabled. At this point, you may want to be sure you are not jailbroken or other thing that could get messed up if it's not stored in your normal backup procedure.
Once you have verified things are fine, you can now choose to start setting up the phone and not restore your backup. This might be the best option if you don't have lots of third party apps that have extensive data. If you do want to restore your backup, you can connect it to iTunes ensuring you don't initiate a new backup to cover the old one or use iCloud to restore your cloud backup.
Hopefully this will clear the iMessage settings and restore things to the way you hope it will work.
Settings>Messages>send and receive. Apple ID is on the top click it then log out. Then turn you iMessages on and select your phone number. Don't log back into your Apple ID until you know it worked. Worked for me.
Then when I logged back in it had my phone number and email instead of just the email from before.