Yeah, money doesn't come here as easy as other games. After passing Naraku you're going to have to focus on farming relics, they'll become more abundant (the higher the star rating the more valuable) and unlike the ones you find in Naraku those respawn. There are other ways to make money, mostly through apps and demon negotiation, but they're not as dependable.
As for the compendium prices, yes they're crazy. To offset them you can gradually invest in the discount app— you can get up to 50% discount. Also, don't overwrite entries unless the demon un question has a rare or advanced mutated ability. Otherwise its not worth it, since they'll take way more macca to purchase.
As for apps:
- MC and demon skill slots are never a waste
- You'll need to max them out at some point. A couple of demon stock slots every now and then won't hurt
- You'd also want to spend some points on MP recovery all the way to party MP recovery
- The compendium discounts is also worth unlocking, depending on your needs and how fusion crazy you get
- Finally the scout app and some of its upgrades is definitely worth it (such as macca gifts and scout+ where they invite other demons to join)
They key is to balance the upgrades to whatever suits your immediate needs.
