v16 has different formatting in the PBS files than v15 did. Off the top of my head, I know that Pokemon.txt now has the Incense property (which shouldn't cause a game-crashing error if you have it in v15, it'll just be space in the file that's not used), and that Items.txt now has a property directly after the name that's used for how the name should look as a plural (this, on the other hand, will mess with v15). If you wanted to take a v15 game and use v16 files, you'd need to update the compiler script section, and any scripts that run on reading the .dat files...