I had this exact same issue with frequent 3-7sec freezing on my 2010 MacBook Aluminium (pro) 2.4GHz. I have upgraded to 8GB of RAM and an SSD, just FYI, but the freezing is still there and very annoying. From some of my notes I had from fighting with the same issue in 12.10, there were two things I remember that might help.
The first two things I did from my notes after a clean install:
Apport constantly errored for me in 12.10, and this is how I fixed it. I'm not sure if it's related to anything in 13, but it's the only other thing I did to the system after a clean install before step 2, so I want it documented in my post.
sudo apt-get purge apport
sudo apt-get autoremove
sudo apt-get clean
sudo apt-get install apport2)
sudo apt-get install nvidia-experimental-310
Those being the only two config changes, my freezing seems to be gone on the Mac now. From what I remember, I had to do a lot more in 12.10 to get the nvidia 310 drivers working, but it seems to be going great after those simple steps. Now.. if only I could find my lost notes on the WiFi driver fix. blah..
I'm not sure if something with the generic Ubuntu drivers causing issues, but I remember my Mac being nightmarish in 12.10 until I got the Nvidia 310 working properly. Unfortunately, my detailed notes are backed up somewhere I can't remember, as all my 12.10 config was done while on vacation last year.
Hope this helps!
EDIT: Nvidia Proprietary 310 drivers seem to mess up the brightness up/down keys. I do not have a solid solution or link on how to fix yet.