The way I see it, there are a few possibilities.
1. Mega Man is not in and is not going to be, and Capcom has not been/will not be consulted. Self-explanatory.
2. Capcom/Inafune have not been approached yet, but Sakurai and co. have already made a character model for Mega Man, with moves and all that shebang, and they will ask Capcom/Inafune for permission later. If they don't get it, they scrap Mega & everything related to him.
3. Inafune is lying, or he approached Sakurai instead of the other way around. Also self-explanatory.
4. Inafune has been bypassed and higher-ups at Capcom have approved/disapproved Mega for Brawl, with or without Inafune's knowledge. Most likely without, since he probably would have to sign a NDA if he knew, and he would have violated it with his statements.
5. Like #2, but no work on Mega has been done yet, and if Capcom says yes, we get another delay for Sakurai and co. to add Mega. I feel this is unikely, as he would have to be integrated into SE and events, have a stage, etc.
Any more possile scenarios? As of now, I think 1 and 2 are most likely.