Have you tried playing both characters in Practice mode to see who you like better?
Amy is fast, but somewhat difficult to use if you plan on powering through dungeons. I find she's more of a support character. She's alright in PvP.
Mari is slow but strong. Her button combinations also take a while to get used to, since she uses a lot of set-ups in order to be effective. Like a tank.
Mari is much harder to get, however. If you're planning on GP missioning it, might as well go for Amy first, and then work your way up to Mari.