It's a good question!

I'd love to have transcoding of analog video to digital video so I could just use the DVI monitor output all the time, even though I recognize exactly why it couldn't be included in the 990 (and why it's not on any other currently-available surround processors except for the Anthem AVM50 and Statement D2 that contain full blown video scalers).

As with many units on your list, the included remote is a fairly basic universal (the same model as provided with the Anthems and the Arcam), which makes it worthwhile to shop around the a third-party universal remote that you like (either Universal Remote, Harmony, or Pronto probably).

If you want to get really nit-picky, I'd like to have the "MUTE" indicator that appears on the front panel display be shifted to just cover the digital input and leave the active input label visible, and I'd like to have a way to find out exactly what the incoming signal format is (mainly how many channels are included in the Dolby Digital or DTS bitstream, since I can tell already whether it's PCM, DD, or DTS).

As for other features that are present or not, a look at my SSP chart doesn't bring anything to mind. There's the always-popular HDMI v1.x support that is still largely absent from surround processors (and likely will be for another year or so, even though the big corporations' receivers are already starting to offer it), but if anything the 990 comes closer than most thanks to the DVI switching that gives full support for HDMI video switching...