I think before this really gets off the ground there is going to have to be some behind the scenes work done. The best way I can think to organize it (and I think similar things have already been suggested, forgive me for not reading every single post) is:
1. One overarching leader, call it a president. They honestly don't need as many extreme hacking skills as they need organizational and leadership skills, to keep everyone on track, put out fires, make final decisions, etc, They would need a base knowledge of every facet of hacking, so that they can understand what everyone else is doing, but...
2. A small core team, call it a board, would be experts in their assigned fields (like mapping, scripting, spriting, storyline, asm, etc), and also have a bit of organizational and leadership skills. The leader would organize the board, but defer to them because they are the experts. The board would also be in charge of making decisions like what game? what features should we implement? And then divvying those tasks out to the appropriate groups.
3. Those board members would in turn have teams, call it a committee, where anyone who is interested can participate, assuming they have at least minimal skills. The committee leader would be in charge of assembling their team (have an application, test, or whatever), assigning responsibilities, overseeing production, and making final decisions, which they would then bring to the board to make sure everything fits with the overall hack.
The way I see it, someone needs to take charge as the president, and gather a board around them to make some decisions before this gets public, like what I mentioned above. What game is being hacked (I would personally choose firered, only because I feel it is the most accessible for everyone of different skill levels)? What features should we implement (phy/spe split? Headbutting trees? fakemon? if so how many? should we use a hacked engine? new tile set? which one?)? And I'm sure more...
Once the basics are figured out, the board needs to decide an order of operations. Should storyline be the first thing created? Should they be working in conjunction with the mappers, or give the mappers the story after they're finished? Are fakemon needed for the story? Get the spriters on it. It's very possible that certain committees will have nothing to do for a long while. All the timing should be controlled by the leader/president, letting committees know when and what to get working on based what others are doing. There would probably need to be some documents accessible to everyone, like currently used space, flags being used, etc.
...anyway. Just some thoughts. I honestly think it's an awesome idea, but would basically have to be approached like an actual game is created. And most importantly, the people involved would need to be selfless about the process, not get caught up in whose ideas are used more, etc.