I think the key here is probably the media player. I'm using the PS3. It cannot stream MKV's @ 1080p for the life of me! Even PS3 media server sucked @ 1080p. Mind you, I'm using Powerline Ethernet... my PC should be more than sufficient to decode it? or to translate it?
Had a little time to look at this. You're at the point I was about a year and a half ago. Transcoding a 1080p file is tough to do for all but the beefiest CPUs. I
think an Intel 2500k
might be able to do it in realtime. I know my AMD FX-6100 will only transcode a BR rip at about 17-20fps which is about 5 frames too slow for doing it in real time. No off the shelf NAS is going to have the power to do this. So, you're gonna have to build your own, get something besides the PS3 or you could remux the .mkvs into .mpg or .mp4 files. The codecs aren't the problem with the .mkv files, just the container. You could use a couple of programs to convert. If you are never going to use them with anything other than the PS3 then go with
http://www.digital-digest.com/software/mkv2vob.html
It'll remux the .mkv to an .mpg file that is completely non-standard and may play back on some other bizarre devices but is really only good for the PS3. It only takes a bout 4 minutes to remux an HD movie and you can do 'em in batches.
Personally, I prefer to us this
http://www.videohelp.com/tools/tsMuxeR
Choose file type of .m2ts and it will remux your .mkv to a standard .m2ts (same as the file type on a BR disc). It'll be a little larger than your original .mkv file but that's normal and it will be standard compliant. Also gives you some options for dumping unwanted audio tracks and subs, etc. Can't do batches but you'll end up with "clean" .m2ts files that the PS3 loves and will playback on most other devices that are BR capable.
But, you'll still have Cinavia to deal with and no amount of transcoding or remuxing will solve that. I dumped my PS3 (and everything else Sony in my house) for a WDTV Live Hub 18 months ago and now I don't worry about transcoding, remuxing, Cinavia, etc. Just smooth streaming. You could probably go with Plex and a streaming Plex channel with a Roku if online services are important.
Hope some of this helps.