The feature that I miss most about my previous DVR (SageTV) is that it had the option to run commercial detection while the show as being recorded. This feature is specifically useful when watching live sports or other live events. If you start watching late, or if you pause while watching, you can still see the entire game and also gradually catch up to the live broadcast as each commercial break is automatically detected and skipped. I really enjoyed starting games about 30 minutes late, automatically skipping past all the commercials, and being caught-up to the live broadcast before the end.
From a technical standpoint, this feature shouldn't be the most difficult implementation, since the Commercial Detection feature is already in place. Instead of running comskip only at the completion of a recording, comskip would run as a scheduled task every 5 or so minutes on the active recording. The .edl file would have to be periodically reloaded by the player to incorporate recently-detected commercials.
The only potential downside would be playback stutters from the comskip process on low-powered servers. I never encountered this issue with my 10-year-old Windows server and SageTV (which also uses comskip), but it could potentially be an issue on some servers. This can be mitigated by running comskip with the "--playnice" option to slow down detection and limit CPU/disk utilization.
This is the DVR feature I miss most, and I hope someday Channels DVR adds this capability.