Any Apps for Surface 2 that can play .mkv files smoothly?

Torrex Plays mkv files very smoothly and is free (or at least there is a free version).
 
I do not understand, why anyone would use an MPEG-4 codec (AVC) but not an MPEG-4 container (mp4). Just to be "different"?

Plenty of reasons. Multiple audio tracks (like if you want to keep your movie commentary when ripping), subtitle support (important for many things, but as an example, needed in Game of Thrones), a wider variety of audio support (if you want to keep DTS, or Dolby TrueHD, or DTS-HD, or even encode to FLAC), chapters, etc.

Matroska is a far better container. It just unfortunately also has a reputation as being a "pirated content" container.
 
Just picked up "Metro Media Player Pro" ($1.49) and it's pretty nice. Plays MKV's just fine.
 
Plenty of reasons. Multiple audio tracks (like if you want to keep your movie commentary when ripping), subtitle support (important for many things, but as an example, needed in Game of Thrones), a wider variety of audio support (if you want to keep DTS, or Dolby TrueHD, or DTS-HD, or even encode to FLAC), chapters, etc.

All this is supported by mp4 (MPEG 4 part 14) as well. (with exception of FLAC maybe, but there are other lossless audio formats supported though)

Matroska is a far better container. It just unfortunately also has a reputation as being a "pirated content" container.

Disagreed. MP4 is quite a bit more powerful, supporting all kinds of meta information on top of the features you mentioned above.
And contrary to MKV MP4 is defacto standard in the industry.
And yes, MKV is the container format for mostly pirated stuff due to the fact that there is much free and non-commercial tool support. So i guess the reputation is warranted.
 

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