My main problems are part of a larger issue with iOS and how they handle metadata.
On my iPad, iPhone, the new ATV, the old ATV and iTunes... they all read the data different. Artwork for videos on one device is the album art, the next its the actual video screengrab. On the iPad, playlists I don't select sync over merely because the items in those playlists are all present. You never know what to expect from device to device.
Also, my biggest gripe with the new ATV: PLAYCOUNTS. Seriously, why no playcounts? I know home sharing is different than the way the old ATV used syncing, but seriously, something that is such an integral part of iTunes is not currently compatible with the new ATV? I find that incredibly ridiculous. That is almost as illogical as the next iPhone not supporting playlists. It makes no sense.
iTunes LP and iTunes Extras not being supported is also a head-scratcher.
Some of my TV seasons are sorted out of order. Metadata for them are flawless.
Overall, I'm pretty happy with the new ATV, but there are some glaring faults. I reckon updates will fix all of these issues, but these are things that should have been fixed before the product even shipped.