Note: This post will be edited as ideas are added.  Dates will be posted on new ideas.

Achievements

Personally, I'm not a fan of game achievements, but, if they're balanced in their ability to be obtain and have an actual worth, it can actually add a fair amount of entertainment and challenge to any game.  There could be player and/or pet achievements that could reward money/items or just recognition.  Obviously there would be easy ones all the way to very hard ones.

New Items

1. Gene-Specific Mutagens (Ultra Rare): I think that name is self-explanatory.  These would be for all different gene categories.
2. Charms: Charms could be attached to pets to provide various effects.  Some items like the Mantle, Scepter, and Ruby Ring could be used as both charms and ingredients,

New Quests

• Item Quests: Besides the quests that ask for you to have a specific creature, how about quests that ask for items?  The reason is because there are only so many structures to create. After a while you're finished with building and you have no need for all of these building items like wood, stone, clay, etc.  There would be two types.  Quests that ask for an items like wood, clay, ink, etc. would have a quantity to them.  Quests that require items that have to be crafted would only ask for one.

New Buildings

• To help provide food for pets, players could build Farms to supply some food.

I love them all. Especially the item quests. It could read "Scholars are searching for a Cartographers Blueprint and a pet to build it". It would cost you materials, and you can't keep it. But you can get rid of extra blueprints!!