Unlike 2013 I haven't played that many 3ds games this year.
Cave story+ and Shin Megami Tensei 4 were only out on 3ds this year in the UK.
One of them would my pick and I'd hate to choose.
Cave Story+ is the best Metroidvania I've played since Super Metroid (Which was about a year and a half ago and lived up to the hype) and I've played many other metroidvainias recently like guacamelee but for me Cave Story+ was the peak.
Shin Megami Tensei 4 was great and has giving me a huge burst of interest in both jrpgs and dungeon crawlers that will probably see me playing a number of others in those genres soon.