The game's Japanese release made use of the Game Boy Advance E-Reader, but the feature was removed in the international release due to the lack of the device's popularity. In the Japanese release, the Request BBS required the use of E-cards and it was possible to obtain Gregar and Falzar battle chips. In the international release, not only is it impossible to obtain these without hacking, but they were broken, causing them to crash the game if used.

Like Mega Man Battle Network 4 and Mega Man Battle Network 5, 6 features references to the Boktai series. Unfortunately because Boktai 3 was never released outside of Japan the Crossover sidequest and most Boktai-themed chips were removed from the international versions. In fact, all the secret chips, the Crossover Program Advance, and the entire sidequest were removed or disabled. However, the sidequest dialog is intact and even translated.

In Japan, there were toy PETs that let you fight Viruses using actual Battle Chips. Because these devices never caught on outside of Japan, certain features involving them were removed from international versions of the Battle Network games. One such example is the Beast Link Gate, which would let Japanese players use their physical Battle Chips in the game. There is even a title screen icon that is impossible to attain without using a collection of real-life Chips.