I absolutely abhorred the Gene Strength and egg mechanic.
Breeding to unlock new creatures was good, but I disliked the hatching. You had an ever increasing cost to gain GS, and it meant swapping entire teams.
I didn’t like the exponential scaling with the system, either.
Having only one nether also meant less customization. I did like having the ability to use a full roster of them in S1.
I would like to see more Castle upgrades, possibly with choices/trees (exclusionary upgrades). So if you want say a spell goblet to customize spells, you lose out on having an attack goblet to customize attack abilities.