I'll probably get yelled at for this but a Boxee Box will do everything except chapters. It may do those as well, I have not looked into it.
There have been lots of complains about BB (as I suppose with any product) but mine has been rock solid. The interface is very wife-friendly, as is the remote that comes with it and the iphone and ipad apps.
I use mine mostly for accessing 4 terrabytes of video on my NAS and for watching Netflix, VUDU, etc. The video browsing experience for local content as wells Netflix is great.
Another virtue is that the BB does a very good job of finding, content on the network, getting metadata for it, and presenting it in an easy to browse/sort format.
FYI I'm pretty sure ATV does not support BD or 3D at the current time, and it is MUCH pickier about media formats than other players.