The obvious:
A5/6
1080p
App store
More specific:
Just enough interal storage for apps. 8gb is plenty for the apps you actually use. I'm most interested in EyeTV (with live or no transcoding). NullRiver MediaLink works okay on PS3, but bad interface (only alpha list of recorded files, no live)
HDMI-CEC, (AnyNet, HDMI control, etc.) Power tv on with atv power, and atv power on when input selected. And the little atv remote is cute and all, but my tv remote is more ergonomic and it has volume control.
BLUETOOTH!!!!! I'm surprised no one has mentioned this! Make that stupid little remote bt, (now hard to aim but could be perfect for your pocket (dj from anywhere). Imagine the possibilities with a bt keyboard and mouse or magic Trackpad!!! Apple tv 1 made your tv and iPod with video, Apple tv 2 makes it a rental/ streaming device... Apple tv 3 could turn your tv into an iPad!!! with iOS safari, mail, etc. Those interactive kid's books would be fun, tooled for gestures on the Magic Trackpad.
I haven't hacked my atv, but I've heard there are apps that let you interface with your iPhone, etc. What if (without jail breaking) there were games that would use the iPhone to control games on your tv. Multipayer with personal info on iPhone. Yeah, just like ps3 and psp, but with 99c games of the month.
DLNA or whatever is needed to play files from a NAS instead of running iTunes on a running puter.
I, like previously mentioned by others, would love the ability to expand via USB. Tv tuner, HDD, webcam. USB Blu-ray drive support would be nice, but BD still isn't supported on full OSX, so keep dreaming for BD on atv.
FaceTime would only make sense with a hardwired external camera, but Apple would only allow it to be an apple cam. Best if it had built in hardware for compression, but if the iPhone can do it, the atv-a5 should be able to handle sd FaceTime. Or just plug in a Kinect! Voice command would be welcome with the webcam, "open Netflix", etc.
I agree that it should have analog audio out. (headphone plug) As mentioned, good for zone 2.
MULTIPLE HOME SHARING!!!!! And TEMPORARY SHARING!!!! FML entering in an apple id with that remote is a pain in the ass! (bt kb!) more important: most homes have more than one apple ID in it, and what if a friend comes over? (first Apple needs to create, then) Allow Quick Share, enter a 4 digit code: slideshow! Video! Music! (I'm happy even if it bans drm'd content, and allows personal photos and videos)