That makes sense, but I don't think you've figured out any thing, nor does what you said only apply to Nintendo consoles. The same could be said with any console that has design problems. If a console has any obvious issues in it's design, then of course the manufacture will try to fix said issues in the next iteration.
Take the PS3 for example. One of it's design issues is it's difficulty to develop for. You can bet your ass that the PS4 will be easier to develop for. In fact, Sony has already stated that future Playstation products will be easier to develop for.
Take the PSP. It has one analogue stick. Look at the PSV, two analogue sticks.
The XBOX had problems too. The obvious one was lack of 3rd party support. MS acknowledged this as an important problem and guess what? They released early in the generation and bombarded 3rd parties. The consoles first few years were loaded with 3rd party exclusives.
You won't find many consoles having the same design flaws as their predecessars.