I have plans. Extra resource packs will certainly be possible, and I'll be open to anything else that wouldn't be advantageous or purposely harmful to the player. But most "modding" will be done via official programs, such as a level/mission editor, weapons editor, creature editor, and maybe even a game mode editor. The game will always run Metroid: Net Mission and its menus, but I plan to include a lot of "in-game modding".
For multi-player, I will probably allow for custom arenas, weapons, game modes, etc., though this will probably be limited to prevent certain problems. I will probably have users able to see all hosted games and automatically download any new or different content in the hosted game they don't have for their convenience, but I'll have to see how well that would work once I get there.
Single-player mode, on the other hand... Hehehe. It's going to be made up of "missions", all of which should be the length of a full game. There's going to be one (or more, I guess) official Metroid: Net Mission mission, along with any user-made ones you've downloaded. I'm planning to make missions extremely customizable from the creator's standpoint, as in you could make Metroid, Sonic, Mario, Zelda, or even Pong. (well, that last one might be hard) I'm still trying to figure out how it'll all be organized, but the editors will probably include a hierarchy of modes from basic Metroid to advanced anything. Not exactly "modding", but..
However, there's always the fine print. These are only what I'm aiming for, not what I can guarantee. I will probably end up settling for less, but you never know...
TOWEL DAY FTW!MIDI-maker / Fangame ProgrammerCurrently doing homework nonstop.