I reluctantly stopped using COW Pro about two years ago when I couldn't get help migrating to a new version of windows. At the time the COW developer seemed to have been busy with new non-chess initiatives. Support may have improved since then.
A lot of work goes into developing a repertoire, and I lost a lot of work. Support is a BIG issue.
COW promotes their own opening books which may be a plus for some users. I import pgn files from various sources for my own repertoire development and training and find that CPT allows me to easily do so. COW has this same capability.
COW also had a min-max capability which is useful to quickly evaluate lines of play. I usually don't rely on that capability. I believe that CPT now also has that capability, but I haven't tried using it, yet...
In terms of uci engine analysis and running your games against your repertoire the two programs are quite similar. CPT offers more flexibility in the training protocols when compared to what was available on COW (as it was when I left it).
COW had a simpler user interface, so I found is a bit easier to get it up and running. However, once I got comfortable with the CPT UI I found the added training capabilities worth the effort.
If, for any reason, CPT were to become orphaned I would reluctantly go back to COW.
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