Nintendo needs to start creating more games with innovative concepts rather than consoles with innovative concepts. New controllers can only get you so far.
I've said this several times before: Mega Man Legends was a niche series, with a niche audience, and it was going to be released onto the 3DS, which is not doing very good. They weighed these variables, and decided that they wouldn't get a return on their investment. This is important; you can't just throw money into a game these days, because that could lead to financial ruin.
And they still haven't given the Engineer anything new since his class update. Robin Walker's favorite class is the Soldier, so of course he gets all the good stuff. Meanwhile, the Pyro gets five nerfs for every new weapon he gets.
Let's look at it this way; Mega Man Legends has always been a niche series. Compared to the other megaman games. Capcom may have seen that releasing such a niche title for a platform that, honestly, isn't doing very good in the sales department woul be a bad idea.
What happened to the art design? It used to be a crazy take on the 1960s, but now it's more like a Free-to-Play MMO what with it's cash shop, but you still have to buy the game.