There are really only a few out right now. The best ones are on their way. I would say Wait until February 7th for "Resident Evil: Revilations" which has a really good online component or March for "Heroes of Ruin". HoR will be the 3DS forst big feature rich online game. It will have a fill drop in, drop out component and feature Diablo type gameplay with very customizable characters and over (I think they said 10,000 different weapons and Aurmors). With a traders network, full spotpass and streetpass functions and other stuff's.
But if you want something out now, I would sugest RE: Merchs if you can find a "cheap" NEW copy. The online play for it is pretty good but limited.