Anything I play with Airplay only gives me stereo.
I wonder what media and in what way do you play?
From below I reckon, your media lib has to be mkv? In that case, you need to try Beamer, which will stream AC3 directly and re-encode DTS into AC3 on the fly. AirPlay most def supports surround sound, but just in AC3/DD5.1 streams.
It won't play any video from a network share. Any media has to be in iTunes. That means having to reencode the media I have. Also, the iTunes interface on the Apple TV3 sucks for large media collections. I have about 600 movies ripped on my home server along with loads of TV shows. As I mentioned earlier you also need to have your computer turned on to play stuff in the iTunes library.
Netshare -True. iTunes - True.
I use Beamer (for non-m4v clips I don't care to convert and keep) or iTunes server to play from NAS share. I keep my server turned on anyway (WWW, VPN serving etc), so it's no additional load to serve media up from the same machine.
MKV and MP4 are quite on par features-wise, but I really prefer the rich metadata in MP4 that makes the media so much more accessible and organisable in iTunes (true, MKV has the same capabilities, but show me a good MKV-librarian?). And iTunes per se is a good handler of a large media library. I have 160GB worth of music, 1200GB movies and 90GB TV Shows. No problem to maintain this library. Navigating it on aTV screen is another story, but there are ways to get things organised (smart playlists, search function, filters like genre/unwatched etc).
Regarding need to reencode - this really depends. As long as your stuff is in HD, it is most prob also in AVC/H.264 already (except for occasional BD rips which have VC-1). Those don't need to be reencoded, just repackaged into MP4 container, which takes not more time than file copying.
For the rest (SD avi files, divx, xvid and other by now not relevant formats), there really are only 2 options: reencode or use Beamer (or the like).
Satellite rips in m2ts format are a PITA in itself, but Beamer can stream them as well.