Aside from 3D HDMI support, I think the biggest improvements would be networking and Airplay. Those features have changed my life. I love just being able to dial up any song/album I want with minimal effort. It's also neat being able to listen to Internet radio stations from all over the world.
As far as per-outs, it does seem to be a feature that is disappearing from lower-end receivers. However, if you're patient and don't mind doing a little work and research on the boards, this time of year tends to be a good time to pick up clearance receivers at good prices. Two years ago, I got two Yamaha receivers at Best Buy (an RX-V867 and an Aventage RX-A1000) for around $400 each. I also grabbed one of the $599 Pioneer SC-1522K receivers from Costco.
If you absolutely need something now, one of the lower-end Aventage units should be under $800 and offer pre-outs.