The second version boards (which are Japanese, not English boards) are closer to straight JAMMA standards. On the 1st board type, there was extra wiring required for stereo sound. I am not sure if Mono was on the JAMMA pin outs or not, but I know that extra effort was required for stereo, at a minimum.
Also, I say closer to JAMMA because they are still not totally JAMMA. The case in point would be the 4th button. JAMMA is a 3 button standard, per player, and the Hyper uses 4. The nice part about this is that a Hyper plugs right into an MVS cab and all 4 buttons are immediately connected.
The one thing you still need to wire though, even if you are plugging straight into an MVS cab, is the test button. The test button is used to set the soft dips for the game you have loaded. Language, and difficulty for example, are selectable in the soft dips.
This really isn't a big deal, although for Fatal Fury, it is a little more necessary. The default settings for that game are just stupid. Each bout is only 1 round, the attract mode is silent and I think it is set to "really easy." Makes for a crappy game with the defaults so odd, so I would wire a test button. The Test for MVS is on a different pin and doesn't work with the hyper.
Anyway, the biggest diff is the sound. Like I said, I know you need extra wiring for stereo. Thing is, you may need wiring for any sound at all. I'm just not sure. My board is the JAMMA Japanese board, so I haven't had to worry about it.