Uh, there's a reason why the 2DS launched at the same time as Pokemon X/Y. Prolonged use of the 3D mode isn't good for the developing eyes of young children, and a large percentage of the Pokemon demographic is young children. It doesn't make sense to have 3D throughout the entire, lengthy game when a ton of the players either won't have access to the 3D mode (because they have a 2DS) or aren't recommended to use it a great deal.

As for Fire Emblem, when Awakening was being developed, it wasn't exactly a flagship series for Nintendo anymore. Sales of each new release had been dwindling and dwindling, and had the sales of Awakening not been so great, it would've been the last Fire Emblem. The main reason it's such a well-received game is because the developers wanted, at the very least, for the series to go out with a bang. If they let one tiny, insignificant detail slide under those conditions, when they were putting so much effort into everything else, I can hardly blame them. It's not at all a matter of "omg nintendo is so cheap and lazy lol".