After actually listening to the podcast and hearing the interview with Inafune myself, I don't feel any differently then I did before. In fact, I feel even more strongly that this gives no indication whatsoever to the exclusion of Megaman from Brawl.
First of all, the translator was, as far I knew, excellent. If the translator was accurately portraying Inafune's intonation and body language, then I would describe Inafune's comment about Nintendo as playful, at worst, and nothing more than a tease. If you actually listen to how he (the translator) says it, you will understand what I mean. That article that someone linked couldn't be more misleading. There is no way you could make an article based off of that interview that was centered around the "No Megaman in Brawl" theme. You totally don't get that from the interview.
Furthermore, while Inafune is the creator of Megaman and the head of his department at Capcom, he is most likely not a pencil pusher -- in other words, he probably isn't the one to handle all of the logistics behind the rights of Megaman etc. Nintendo may have not spoken with him personally, as that, taken literally, may be wholly unnecessary.
I am just saying not to get so down in the dumps about this podcast. Actually, the podcast was very enjoyable to listen to. It's just that article that was written about the podcast that totally blows it out of proportion. With that said, I don't think Megaman's "chances" are either worse or better off after this whole thing. He's either in, or he's out, and I'm betting he's in.
If he isn't, though, it won't be the end of the world. Disappointing, very much so, but there's so much more to look forwards to then have one character's lack of appearance ruin the rest of it.