You can basically think of version B as a time skip after A considering its a completely new location with all new girls but the same protagonist and abilities unlocked from A. There is no lore in the game so there's no real need to play them in any order other than wanting to see how he got all the abilities from A that you use in B. It was just a patch job as a temp fix of a long term issue that'll only be fixed by a completely new game built from the ground up in a better engine.