Being "unique" isn't what's cost Nintendo. On the contrary, the "uniqueness" of Nintendo's offering is what makes them stand out from the crowd of the gaming industry.
Their main problem is a failure to understand their market, to keep up with industry trends and to nail the fundamentals. For instance, their online infrastructure is weak and they've taken time to get it up to industry standards. The courting and consultation of third-parties is now a basic element to console development but their failure to engage with them has lead to a underpowered console third-parties prefer not to develop on. Being late to HD development and not paying attention to the issues other devs have faced when making the switch to HD has lead to delayed releases of big games on Wii U.
When they've succeeded in the home console space, it's normally because they've managed to differentiate from the crowd to such a degree that not having core features of the other consoles isn't that big of a deal. Innovating is a good thing, but they need to nail the fundamentals as well.