The 9000es is better built and has better SACD playback. CD playback was good with the 9000 but not great. Same for the 999 although it could actually be not as good(I didn't spend a lot of time listening to cd's.) I prefer a separate cd player.
Video is equal to or a slight edge to the 999. So, if I was interested in SACD go for the 9000es otherwise the 999 is as good or better in the other facets. The 999es is certainly not the over achiever and over built like the 9000es is however.