If this was happening around the midpoint of the season instead of the very end, I might believe it. But even with the final episode being as long as Richie says it is, there just isn't time for Mario to leave, save Luigi, and then go back and get the Master Sword with all the rest of the stuff that has to happen before the end of the series, and any other way of killing Ganon after establishing nothing can would feel like a deus ex machina. The only thing I can think of that wouldn't seem like an asspull is if Link showed up with the Master Sword afterward, but even that's not without it's share of issues -Why spend so much time on this Mario-gets-the-Master-Sword subplot only to give it to someone else at the last minute?
I also, and no offense to Richie about this, feel that there is such a thing as too much Mario. While Mario may be Bowser's rival in the games, as far as the show (or at least season 5) is concerned Luigi is. Luigi's whole arc this season has been about having to stand on his own now that Mario is gone, and having Mario save him at the last minute would go completely against that. Mario will likely be the one to beat Ganon in the end, so letting Luigi have Bowser isn't that much to ask, is it?