Yeah, it looks like there are a number of problems to me.
I've been trying a number of things, but I can't get it to work as advertised. Replies come back to the wrong device, nothing is synchronised and sometimes messages fail to send. I assume it's teething problems, but Facetime is still totally unreliable (and therefore unusable) so I hope Apple dont make a hash of this too.
I've ensured that I am using the same Apple IDs everywhere (which is hard as I have one for my iTunes account and another for iCloud). I assume it's the iCloud one that needs to be the same one the iphone, but to be sure I created an iTunes account with the same ID so I'm logged on as one now. I realise this will create problems for me in the future as I already have 2 iTunes accounts (1 UK and 1 US) so updating apps on the phone is a total pain.
Things I'm finding:
1) Messages aren't syncing between devices.
2) If I send a message from OS X to person B, the replies are going to my iphone. If I send them to person C, the replies come back to the desktop. Never both (like it should) but always consistent.
3) Messages sometimes fail to send
4) iOS messenger app 'forgets' my Apple ID
5) When I tell the iOS app about my Apple ID again, I have to add the additional email addresses again
6) OS X app doesnt give me the ability to set my phone number as the caller ID