I'm extremely impressed with how much is here, you've pretty much nailed the base design of an expansive RPG. As for the gameplay and story, for what you've accomplished in such a short time, is very commendable. I think the inspiration is very apparent within while maintaining it's own style to a degree. Also the design of the main character is nice, maybe down the line you'll be able to replace the base designs with your own, which I think will look a bit more cohesive than it is now.
Oh, and the gene equipment implementation is possibly my favorite part, since it's almost like a fuse between FF9's equipment/abilities system and SMT: Nocturne's magatama system.
One MINOR 'bug' I ran into was when I selected a specific entity to be healed and switched a different entity out in the same round, the entity that occupies that space got healed instead of the one I wanted. I think a quick fix may be that when switching out entities, you don't put them at the end and have the rest move to the left once, instead just switch them out in the space the switcher occupied. It could be a limitation of the software itself, but I'm sure there's a fix.
Some minor critiques/additions I would suggest is:
- Probably show the max for HP/MP in battle or in menus rather than when only switching in entities.
- Add some kind of weakness/resist types somewhere in the status of entities rather than guessing (though most of the visualizations are pretty obvious, like books are weak to fire and robots are weak to acid, etc.)
- Most areas are a bit too expansive, where I believe it's really only accommodating the 'random' battle implementation, if you shorten its time, with a tad more battles, you could have tighter areas.
- Finally since the inspiration is very heavy maybe think about adding in a skill point choice system after level-ups like in other SMT games or something fairly similar.
To sum it all up, what you've got here is definitely an A+ in how well everything is presented with great gameplay, intriguing story, and complementary inspirations from both, especially within the allotted time. Superb job.