I don't think this is your problem, but it might be and doesn't seem to have been raised elsewhere. I bought a new MacBook Pro running Lion a few months ago, and found that the (also new) Magic Mouse would not connect automatically—I had to force it to connect after any disconnection from switching off the MM or from rebooting the MacBook.
One of the genii at the Genius Bar, after ½ hour of experimenting and in the process of telling me that Lion would have to be reloaded, suddenly realized that the MM connected upon being clicked. He stated that he had not run into this before and that it must be a new feature in Lion related to battery preservation.
Bottom line, try a single mouse click to initiate the Bluetooth connection.