It's been a little while since we last checked in with Team MMBN3D. Fortunately, good news is afoot! Work on Mega Man Battle Network 3D continues... and there's going to be classic local multiplayer available from day one.
Much like the GBA games that inspired it, MMBN3D allows players to use a large library of Battle Chips. A variety of playable Net Navis will be available at your disposal, including some that have never been playable in any form (oooooh!).
As for the prospect of online multiplayer, it's not in the cards at this time. Team MMBN3D says it is indeed a possibility but not for a long time. The focus right now is getting the game out the door, so to speak.
MMBN3D is targeting a late 2016 to early 2017 launch window. You can follow the game's progress on Tumblr and Twitter in the meantime.