[r0lZ]

Sneaker_ger is right. But you should also take into account that the resolution of the image is divided by 2 in one direction if you encode in Half-SBS or Half-T&B. Therefore, in addition to the re-encoding, there is also a quality loss in resolution. (To avoid that problem, you can encode in Full-SBS, Full-T&B or Frame Sequential format, but that formats are not supported by the majority of the hardware players.)

Most players do not recognise at all that a MVC-MKV contains a 3D movie. They play only the AVC stream, in 2D, and ignore completely the MVC stream. As fas as I know, only Stereoscopic Player is currently able to play the MVC-MKV in 3D. I don't know if it can play it in 2D, but you can use another player anyway. In the other hand, almost all software or hardware 3D players can play the Half-SBS or Half-T&B formats generated by BD3D2MK3D in 3D. It's why I wrote it. Most players or 3D-TVs have an option to display the 3D movie in 2D, except some software 3D players. And, of course, you cannot use a 2D-only player to play a 3D movie generated by BD3D2MK3D in 2D, because it will show you the two views at the same time.

So: Use the MVC-MKV generated by MakeMKV if quality matters much, if you have plenty of disc space, and if you are happy with Stereoscopic Player to watch your movies in 3D. You can watch them in 2D easily, without quality loss.
Use Half-SBS or Half-T&B created by BD3D2MK3D if you want a format recognised by all 3D players or if disc space matters. It may be more difficult to watch the movie in 2D on a PC, but it's possible with the right software.