In my opinion, the number one thing Nintendo should improve the most...

[TheWPCTraveler]

I'm fine with the eShop, though. I speak as someone who looks at the entire operation from the perspective of a dev.
If the majority of games drop price far less often, it's much easier for someone to benefit from a price drop.
Besides, I'm not worried. Once I hit 17, I can snap up all the Atlus titles because of their sales!

As for what I'd like them to improve, I'd say it's good enough if their next-gen successors are simply more powerful versions of the 3DS and Wii U. The latter is because the four-Gamepad system is amazing, if you think about it.