No ROMs based of anything other then tw have the functionally that your looking for in terms of the spen. With that said, you can get some decent apps that make it less painful.
When I run cyan or any other AOSP/AOKP ROMs I install spen launcher along with notebuddy and cm spen add on. That combination will allow a pop up menu when you remove the spen that allows you to have access to your spen apps. As stated papyrus is a good one, gnote found here on xda is another, write and sketchbook, you can backup or extract sketchbook from stock ROMs and it installs fine.
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