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You should go onto the Apple Support Community section and do some searching...
https://discussions.apple.com/community/mac_os/os_x_mountain_lion
I can almost guarantee you'll find the same issue being discussed, and hopefully a solid solution as well.

As far as mail notifications go, you could set the mail app to open up automatically when you login/turn on your Mac.

As far as iMessage goes I wouldn't expect iOS 6 to solve any issues. Sure it will unify a phone number with the apple ID, but that just means more messages. I've just turned off iMessage on most of my macs as I use my iPhone for it.


Sent from my iPhone