Cyanogen pretty much is the stock ROM. It's built from source with minimal changes. Almost all of them are usability tweaks and security patches.
The nice thing with the Nexus range is that as it's directly from the Google source, you don't have to worry about the issues with battery drain and driver issues that you get on other devices as much. The reason so many ROMs on the S2 and such have issues, is that Samsung optimise their ROMs with endless hidden tweaks and features that you really need the source to know about. As soon as you try and build from the Google source, you hit the problem of these not being present, hence, worse battery life in some cases.
Heck, the battery saving features in Cyanogen are nice. You get more control over the CPU, lock screen battery drain and so on....
Believe me, I was in the same boat for a long time. But as soon as you realise Cyanogen is nothing more than the stock Google source that is used for the Nexus branches, along with minor tweaks it's a lot less daunting and worrying