"publishing rights expire after a time."
Publishing rights don't really expire in games. They can be sold, leased, or end based on contract terms, but they don't just expire based on time. In the case of Mass Effect, Microsoft very simply looked at the numbers, saw that ME1 made them a small amount in its fifth year, EA offered them significantly more for the rights going forward on other platforms, and MS said "No brainer. Sold!".
Publishing in games almost always includes ownership. In this case, Nintendo probably funded a good 25-50% of the game's development cost. If they hadn't, this company that always makes multiplatform titles wouldn't have stuck with a single, small, unproven platform. History shows their preference for wide release.