Rune Factory 4 and Fantasy Life. Both have lots of customization and are feMC capable. The former is similar to harvest moon but they added combat and sprinted with it (it's combat focused). The latter is similar in gameplay minus the love-interest, and is a pretty happy, easy-going game. Only the post game could be considered even remotely hard- I still had a ton of fun with it the whole way through. Both also have major crafting systems.
Gotta plug 'em Atlus titles too. The Devil Survivor remakes are both tactical rpgs with demons. Plenty of female characters, and lots of customization. Fusing is love. I would say smt4 as well, but a sequel has been announced and you may be better off waiting for it instead (smt4 is male MC only too).
Totally agree with Patrick on EO as well. It's... a pretty unforgiving series. EO4 is definitely the place to start. Don't forget to pet the deer!
Edit: EO is a first-person dungeon explorer. Town is menus only. Create up to 25 characters over 10 classes for EO4 (3 are unlocked through story progression), and allows for sub classes. Dungeons are explored with <=5-member teams. 1 post game dungeon which is always a pain; iirc EO4's doesn't have a teleport maze at least, and multiple post-game bosses + superboss. EO4 is one of two entries in the series that also allows for exploring the overworld.