I doubt that phono was dropped as a space issue - I suspect it's more of a cost issue.
The Model 990 is based on a platform that is now more than four years old (maybe closer to five years, actually) - it was probably more appropriate to have that many of these inputs at the time the platform was designed. Looking at this page , I don't think we're going to see as many "entry level" analog inputs. I'm going to call it four analog AV inputs and two analog audio inputs. Those likely serve two purposes: legacy support (for the VCR's, LD players, game consoles, SMS-1's, and the like) and "defining" inputs. Historically, we've grafted coaxial, optical, component, and DVI/HDMI inputs on to the basic inputs that were initially identified with each of those legacy "entry level" connections. And before we get too upset about the "high" number of these inputs, let me toss out this thought: those four AV and two audio inputs are not enough by themselves to let us fully use the array of other inputs that surround them. Sure, the multichannel analog input is probably a separate entity, but that still leaves half a dozen coaxial and optical inputs (or one for each "entry level" input), three component inputs (almost one per "entry level" input), and four HDMI inputs. For that array of "upper tier" inputs to be reasonably useful in a large system, we are likely to need at least a couple inputs that are independent from any analog stereo connections. If they do something like that, it would be a first significant step down the road toward limiting those legacy inputs to a couple connections over in a corner. It is not something that has really started to catch on yet - I was looking at the rear panel diagram for an Onkyo 885 processor recently, and there are analog stereo for each input plus composite and s-video for each video input.

Another thing to think about in this equation: the second zone, which is typically an analog pre-amp with rudimentary video switching - for that to work, you need to either include some of the old connections or you need to figure out a way to have a parallel DSP section and extra DAC that can steer all those digital audio and video signals to the second zone.