Lee's initial suggestions are pretty good. Item 4 only being an option if 2 were already added, of course, and even then I think it might be worth retaining. I also wouldn't mind seeing a bypass mode for the 7.1 inputs, although from what I understand they've pursued that in the past and run into some problems implementing it.
6. DD, DTS, PCM, and DPLIIx should be separate surround modes in the menu. Selecting DD decoding would help with sources such as cable boxes and DVRs, considering the 990 takes about half a second to lock in the signal and some premium channel movies don't have a silent pause at the beginning (about 1 sec) like DVDs. Also, some digital outputs (i.e. DVD) are better than others, so the 990 may take even longer than usual to lock in the DD bitstream. As it is, I miss the first 0.5 secs of my CDs' first track unless I stop and replay or go analog.
7. A separate auto mode (not a surround mode per se, but a setting in the menus) that will lock in a signal and select a processing mode for you, just like the 990 does now. All you do is select auto and the processing mode you want.
If I understand this one correctly, you want to offer a way to disable auto-detection. This really isn't an option, especially for devices like cable boxes - the 990 needs to be able to determine if the source is DD, DTS, or PCM, and a cable box will regularly output DD 2.0, DD 5.1,
and PCM as you move between channels (or even between 2.0 and 5.1 when going between programs and commercials on HD channels).
On the other hand, the 950 used to offer a mode that would allow forcing a specific decoding mode. That option was
only a safe approach for a source like CD for which the signal was assured to always be PCM - locking PCM would be most unfortunate if that input ever happened to encounter DD or DTS bitstreams.