Does anybody else HATE this about iMessage?
When a friend iMessages me, the iMessage my phone number, NOT my Apple ID.
With Messages for Mac, you don't have a choice but to send from your Apple ID, creating two separate conversations or threads in Messages on iOS.
If you're iMessaging somebody on a Mac from your iPhone, and you lose your 3G or WiFi data connection (every so often you'll see that message that says "Sent as text message") you're screwed. Without a data connection, you can't reply to somebody using Messages for Mac, because it goes through the iMessage protocol.
Apple should find a way to integrate your phone number in iMessage for Mac (and iPad and iPod touch provided the user has an iPhone) so there are no double-conversations in the iOS version of Messages.