For some minor experimental hacks, GM and I (where GM did all the work) tried 2 things: trying to get BN5's Navi Change back in BN6, and trying to get BN5's Operation Battle mode back in.
Here is how it went.
In BN5, you can Navi Change similar to the DS version. In the DS version, the values for it were re-purposed for the game's exclusive Navi Change system. Originally, slotting in a Navi Chip through the Chip Gate would allow you to change Navis for after exiting the Custom Screen. Though the same values exist in BN6, this feature was obviously removed. All the relevant routines were also removed. Putting the code back, Navi Change can be brough back to BN6!
Looking into Operation Battle, I wanted to know if it was possible to restore it in BN6 as well. After all the graphics are still in the game and referenced, so it couldn't have been too far removed. Once again, the value that normally enables it is still there, and behaves in the same way, too. There would be no apparent effect in battle though. Following some relevant routines, the special value 0x40 which is written exactly the same way as in BN5 can be used to force its effects mid-battle. This reveals that Operation Battle was re-purposed to be a Chip Gate mode in BN6.
The reason this didn't work from the value before is because the game now requires additional hardware checks to even be tricked into this mode. To remove the check, go to the following offset and change the following bytes:
0802E142: C0 46
After that, change the byte at 02001F6C to 20. Chip Gate mode in battle is now enabled.
Unfortunately, short of writing a virtual Chip Gate, this is as far as this hacks will go. Personally, I would have liked to see Operation Battle mode in BN6 but clearly it's not coming back. Without a battling AI, you're sort of doing 2 things at once in a real-life Chip Gate situation.