A few thoughts on somewhat-related things that would be useful, since you're working hard on the system...
1) The ability to customize channel-lists on a per-tuner basis, and the ability to specify a "preferred tuner" would be very useful. Perhaps this is already possible? If not... That way, if you have a particular tuner that handles HD, you can specify HD channels are ONLY available for that Tuner (even if the other tuner can technically use the HD channels, perhaps in the case of an external tuning set-top box). You would generally set MC up to "prefer" a secondary SD-only tuner (so that it is generally used for less important jobs). However, any programs that you specify to record only on an HD channel, would automatically use the HD tuner (because it is where the HD channels are available). The ability to set this effect manually, can come in handy as well.
2) Customizing start/end time "padding" on a per-schedule basis is very useful.
3) Along the lines with the "padding", it is equally important to have the padding be able to work smartly for scheduled recordings that occur in sequence. So, say you want to record the following shows on HBO in sequence: Entourage (30 min, 8pm), Summer Heights High (30min, 8:30pm), True Blood (60min, 9pm), and then The Life and Times of Tim (30min, 10pm). You want the padding for Entourage to be Start 5 minutes early (so you don't ever miss anything), and the end time for the Life and Times of Tim to be 5 minutes late (same reason). However, you don't want to have to worry about going in and setting each other show to start/stop exactly on time (away from the defaults). It is useful if the application recognizes that they are sequential recordings all on the same channel, and automatically adjusts the start/stop padding times to "encourage" them to all be recorded with the same tuner. This will prevent the system from "toggling" back and forth between two available tuners, or worse skipping recordings, only because they "seem" to overlap by a few minutes due to the automatic padding when they obviously cannot because they are sequential. This is a major failing of most of the software DVR applications I've used (some do better than others, but none are quite perfect).