This game is much better than the first one. It's very admirable that you took almost every part of that and improved on it. Unfortunately, it still isn't good. It has a lot of shit keeping me from recommending it. The grind is the biggest hurdle because it isn't a fun grind. It feels arbitrary and not well-scaled.
Fuck you for making the grind for materials needed to build shops in server city such a pain. You really should've had a couple of recruitable digimon that upgraded the lumber mill and quarry or have some more early game uses for the wood and rocks so I had more of an incentive to stock up on them before I needed 50 Digihardwood.
And why did you bring species exp back? I don't think anyone likes it as it just adds another value you need to grind for. You didn't even properly distribute all the sources. Aquatic and dragon exp are plentiful at almost all levels but beast digimon are only common at low levels. You forgot to give a reliable option for grinding mid or late-level beast and bird EXP. You might want to change what spawns in a zone or two if not make up a new one to fill that void.
Also, the combat sound effects are still kinda poor. You're already "stealing" designs and assets from other games like the pokemon orbs and the challenge mode stadium being a freedom planet background. Why not steal the sound effects from Megaman Star Force or Fossil Fighters? Those games had great sound design.
Whether you think my criticism is worth listening to or not I want you to know this game of yours has potential it just needs refinement.