Moving a folder from Mac Pro to new MacBook Pro

I have a new 15" retina MBP and an older MacPro desktop, both for work.  I like to move my Mail folder between the machines - to the MBP when out of office then back to the Mac Pro when I return.  I was able to do this easily via Firewire with my older MBP.  When I connect via the Thunderbolt to Firewire adapter, I can see each machine but that's as far as it goes.  I cannot connect and therefore cannot transfer the folder.  I resorted to using Target Disk Mode, but I don't want to do this every time.  MBP is running Mountain Lion and Mac Pro is running Lion.  Any thoughts?

I've got a time machine backup on an internal HDD that also contains a partition for bootcamp and a partition for scratch use with photoshop cs3. I also have an external HDD for use with superduper. It has one partition for my startup disk and another for my home folder.
However, I don't know if the time machine option will work for me as it resides on an internal 3.5 HDD, unless I can somehow connect the macbook to the mac pro via ethernet and copy the time machine data that way.

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