I think this research done by Ron Carmel, co-creator of World of Goo, shows that Wii/DS/3DS/Wii-U owners are kind of screwed when it comes to future indie developer games on Nintendo platforms, especially if you look at this graph.
Sure, his post is about developers migrating away from XBLA, but it goes on to show data that getting your game to market with Nintendo is extremely difficult (but still not as bad as with XBLA).
At least this might at least answer the question as to why there is still only one 3rd party eShop game available for the 3DS six months after the system launched.