Sorry for the delayed response. I completed the current content and then wanted to go back to replay the game with the knowledge of where it was going.
I agree that the third layer should be reworked. It feels like it is replacing everything from the second layer with something that is almost identical and doesn't feel very satisfying or new. I wish I had some ideas for you, but unfortunately I don't.
Playing through the game again I remember that the Goddess raids need some tweaking as well. Easy and Normal seem pretty good, and when you get to Hard you're flying through them with like 1 second battles. Then once you get to Extreme everything comes to a screeching halt, and I had to stop playing on my second playthrough because it was taking too long. Each battle is >1hr, and progress isn't made unless the tab is active, even with the Providence upgrade in the blue skill tree. I confess I'm playing this game at work, and I can't leave the game open front and center on my screen for hours at a time to get through the raids. I think when I played through the first time I actually took my work computer home and left it running overnight to get through the raids.