Understandable, but as Zenith pointed out, your three top players end up taking votes away from each other. But even then, I'd say all three also received a boost from your record. Based just on how well players played, I expected the MVP to be either Anaya or Vereker. And while being the conference champ helps, the fact is you only had 3 more wins than the Jack Rabbits, so it probably wasn't that big of a boost.
If you only had Eckert or Wakatsuki, the one you had might have had a better shot at winning because that one would have been your go to guy every game. But then you probably wouldn't have the record you have. It's a cruel trade off, and perhaps not completely fair.
I think it is difficult, and more so as you move up in the divisions, to both have the best overall record and have the league MVP. And in fact if you look at the NBBA and the four D.II leagues in the US, you will see that none of the MVPs are from the team with the best record. If someone were to focus on winning an MVP trophy (and I clearly may not be the best one to talk here, as I doubt I'd ever build a team with a player capable of winning an MVP), I think they need one clear stud and then 2 or 3 high quality support players. Guys who will help the team win and feed the stud, but are unlikely to take a game mvp title from the stud at any point. And of course, the stud needs to play in all 22 league games, rather than being used in cup games.