I would say Earthbound. (Not Earthbound Beginnings.) It has a nice story with a lot of funny remarks and dialogue. Though it's a little long and can get creepy at times. Either that or save up money for other game, but its your opinion.
I would recommend the recent Mighty Gunvolt Burst, if you like retro-Megaman.
The rest, just look up at the eShop discount sales and see what games caught more your attention.