Like Battle Network 4, each region has a different logo and title screens. The Japanese and North American logos are notably similar, but the European logos follow the style of the previous games released in the region.

In the Team of Blues release, the Japanese version of Team ProtoMan, there exists a menu for using the Wireless Adapter, rather than the Link Cable, for multiplayer play. It's possible to access this menu through the use of hacking tools, although the feature is not actually programmed. Both the ProtoMan and Colonel versions can use the Wireless Adapter for the Crossover Battle with Boktai 2: Solar Boy Django, so it's unknown why this feature was dropped from the main multiplayer section of the game.