I feel automapping would change the tone of the series a lot. There's a reason why games which are very similar to EO like SMT SJ and Persona Q still don't -feel- like real EO games. The manual mapping absolutely contributes to the exploration experience in EO games. Even without dual screens, I feel it is a series which will always need to be on a platform with a touchscreen to replicate that experience.
My problems with Persona Q was more to do with the automap and more to do with the fact I don't think the battle system was nearly as balanced and I don't think the dungeon visuals were very interesting.
I can see why someone would think mapping made the exploration experience, but I think you can replicate at least 90% of that if you just have good dungeon design.