I guess you're right - Inafine doesn't have every single piece of info bout Mega Man. So baiscally, we're to assume that he holds this info, even though he doesn't?
You're missing the point. You shouldn't take Inafune's statement "We still have time left" (to put him in) literally, because that would be ludicrous. If Nintendo had REALLY not started any sort of work on implementing megaman into brawl, less than 2 months would be enough time to get his boots done. Maybe.
That's just a silly example but you know what I mean. Inafune is a game designer and has even recently been working with very complex 3d games a la Dead Rising, Resident Evil 4, and now Bionic Commando (which I am stoked for). He knows what it takes to do this or that in the industry so making comments that just make him look stupid probably isn't something he spends a lot of time practicing.
No, what I think is going on here is that Inafune does indeed know exactly what is going on with megaman and brawl and is simply refusing to let out the details. He never actually said "megaman isn't in brawl", he said "nintendo hasn't called me". Some people, including myself, have already brought up the logistics of that statement: Nintendo probably doesn't actually speak to Inafune when they want to use a CAPCOM character. Like I said before, Inafune is not a pencil pusher, and Nintendo, more likely than not, does not have to get permission from him.
So yes, if you take Inafune's statement "we still have time" literally, then you would be quite right in your assessment that there is no way megaman would make it into brawl (assuming no work had already been started). That's a no brainer. However, if you take Inafune's statement with a grain of salt and note the fact that it sounded like he was hiding something, it doesn't take a rocket scientist to realize that there is "more than meets the eye" with Inafune. He probably knows megaman is in Brawl but is simply beating around the bush, because I'm sure it's up to Nintendo to release that information and not Inafune.