things off the top of my head that have changed since then:
Multiple species revamps
Ferrikki released
Lost Grove (post-available plot area, lv60+) released
Proficiency system entirely overhauled (level up points no longer exist, proficiency point gain entriely changed, all element attacks reworked and adjusted, move ranking changed from putting in prof points to getting move exp when fighting in lost grove)
Equipment overhaul (eg, relics now always give Damage boost that matches the equip type, general stats on all post-overhaul equips are better, warden and crusader gear is retired and no longer drops)+ Lost Grove gear added (equippable to lv60 pets)
Nurture system redone and streamlined
Many more restricted trait sets added + Lost Grove res traits added
Base mana can now reach 200 via breeding
Prismatic philter updated to include mana
New philters added for Health and Mana
Pets can now be bred to be Supermax- that is, base stats can be higher than 2000/200/100/100/100/100, via the introduction of Wild/LG stats (pets caught in lg have +__ stats after their base stats. How high these are depend on the pet rarity, both TP count and if the pet is themed or not. Legendary+Mytical themed pets can cap out at a whopping +75 at the highest in any of the four base stats (the stats are random within a range for each pet). The stats drop with each generation they're separated from the lg pet.
Example:
Legendary unthemed grove pet and her
great-great grandson
All festival zones have gotten new, larger maps
Pet growing activity during fests altered slightly
probably other stuff but can't think of it right now. That's a fair amount of the things that have changed though