Here's an idea I came up with while tweaking a lot of my items. Screws mode.
This mode would replace most likely replace CTF. Each team gets an Auto (or Reggae/Dr wily for wily team) spawned at either end of the map (for this reason it may have to replace CTF). The idea of the game is to kill the opposing team members, which results them in dropping screws. The goal is to take the screws back to your "auto" to earn points. If you die however, you spew out all the screws you had. First team to hit the point limit wins!
Other things to make things interesting: Auto could give you rewards, such as powerups, weapons etc (maybe even upgrades unseen in MM8BDM). He would give you better rewards (i.e gravity hold) if you bring him lots of screws in a bulk!
Huh. Sounds like(what with the pointlimit and all) that it would be better as a Teamgame mode than replacing CTF.
All right, here's my idea;
Uplink Mode. Essentially, it's a crossover with MMBN for the sake of getting Skulltag mode and runes into the game.
The objective of Uplink mode is to grab the other team's blueprint data(a recolored Possession memory chip) and uploading it at one of the I/O points scattered across the map. Also new to this mode is Upgrades(resprited runes) that up your speed, jumping, and attack stats. Unlike other powerups, you can only have one Upgrade at a time, and it only goes away when you die.
Of course, to avoid breaking the "inside the computer" gimmick all of the maps would have to be cyber-themed.