The most common answer is that 3rd party developers have a hard time competeing with Nintendo first party titles. There are a limited amount of games most people afford to buy (an attach rate of ten games per console is considered good). Of the 37 most sold 3DS games only 8 are from other publishers than Nintendo (Monster Hunter, Yokai Watch, Dragon Quest, Kingdom Hearts, Puzzle & Dragons).
Shin Megami Tensei has a hard time selling on 3DS despite good reviews and frequently occurring sales (€10 digitaly in Europe).







