Others have touched on your other points, so I wanted to address this:
Switch to a standard .mp4 container. Much better supported on hardware or software. Some day you will want to be able to stream from your server to a thin set-top box or load a file on your kid's phone. On that day .mkv will make you cry.
Plenty of thin set-top box clients play mkvs already. Devices from Western Digital (WD TV Live), Netgear, Seagate, Roku, Popcorn Hour, Boxee, and many others all support mkv out of the box, with header compression support, subtitles, chapters, multiple audio and video streams, and some even support 3D (not the new mk3d format yet, but SBS works) and will play subtitles correctly. Most mkv files contain MPEG2, h264, or VC-1 video and AC3 or DTS (or the newer Dolby TrueHD, DTS-HD, etc) and all of these players handle those just fine. Don't blame the container for being flexible enough to allow any random codec. Blame whatever crap source you stole your videos from for using a random codec. Those of us archiving our DVDs and Blu-Rays will either encode in H264 or remux the original MPEG2/H264/VC-1 streams untouched and have no problems.
If you want to move videos to a phone, that's easy enough to do. The beauty of being a completely open container format means that it's trivial to demux Matroska containers into their component streams, which than then be remuxed into mp4 for devices that suck. Since you'll probably want to down-res the videos anyway for handheld formats (even on tablets you won't want higher than 720p), there's no reason to keep the originals in mp4. Keep your original, untouched videos in mkv and re-encode at lower resolution and bitrates into mp4 using Handrake for mobile devices.
Divx (yeah, whatever, they're still relevant) has adopted MKV as their HD container format, and the proliferation of "networked media tank" devices plus Matroska's openness makes it not only relevant but desirable for long-term video storage. Using 5+ year old devices like Xbox 360 and PS3 as your benchmark for what containers to use would be a bad idea (Xbox still doesn't even support 6-channel AAC in mp4, never mind supporting AC3).