Nintendo wants to keep games prices high, which means they don't want little 99 cent indie game experiments on their system. The problem is I'm not going to stop buying those 99 cent games. I'm still going to shell out premium prices for first party Nintendo titles but now instead of wasting money on a $30 throwaway game for my 3DS in between big releases I'm just going to download some cheap time waster for my iPod.
So the biggest problem is for third party developers. Nintendo is trying to comfort third parties by telling them that they still have a home on Nintendo consoles. Unfortunately most people own a console in a addition to an ipod or smartphone and those devices are only going to get more and more popular. In my mind Nintendo (and MS and Sony, for that matter) should embrace the stupid little throwaway games and let third parties deal with it. In the end the market will dictate the types of games that it wants, and I think there will be room for all sorts of different price points.
I think the best solution is to move away from the tradition of releasing every game on a console at the same price....right now it's $60 for an Xbox/PS3 games, $50 for a Wii game, $40 for a 3DS game, etc. Occasionally budget titles show up, but even those are all the same price ($30). The App Store and Steam have taught us that lowering the price of games in general and providing a continuous spread of prices from $1 to $50 is the best sales model.
Wow I've gotten off topic. IN CONCLUSION, Nintendo should support garage developers that sell 99 cent games, independent devs that can charge $5-20, and premium devs that can charge $20-40. There is room in the market for all of them.