It's only popular in America, not Japan. And Nintendo focuses on Japan. Plus, the game of American football is a bit rough, and not very family-friendly. That kind of style certainly didn't work out for Mario Strikers Charged, as it has a dark and depressing art style, and the characters seem mean-spirited and unlike themselves. It is no surprise it is one of the worst-selling Mario games. Also, football has 11 players on the field for both teams. That's 22 Mario characters already, so there's no way to have a bunch of different teams. Mario baseball was already stretching it with 9 players per team.
It could certainly happen, but I still have my doubts. After this though, there aren't many sports left. If we do see one, it would be widely changed, more family-friendly with altered rules and less players. Which would be fine with me. It does seem weird that they created one based on that manga, but there may have been a reason for it. I wouldn't know.