If I understand it correctly, the approach taken by the two are a bit different:
Adrynalyne's Vanilla starts with a leaked version of the stock htc rom, strips out the a much of the htc junk as possible while keeping things performing fast and stable (basically rosie? - the launcher + widgets + clocks. Most notably, the phone-related components - dialer, logs/contacts, phone screen, answer screens - are still htc).
CM seems to go from 'ground up' type of approach, adding to and modding a vanilla version of android. It is very much vanilla, which a number of nice but typically controllable tweaks. This includes a vanilla style dialer, phone, contacts, etc. With the current stable version, it seems the most notable missing component is the camcorder.
Currently, I am running adryn's pbnj2, which has been working very well, save for the htc phone related issues (mitigated by some add-ons, but not yet to my liking). My biggest problem is that I have invented how I want the phone to look and function, but it is almost a hybrid of the two. In order to deal, I might just take some vacation days and try to develop my own solution.
