I have two ideas, mostly based on other games but might work nice here anyway.

1.        What about alchemy? There is a plenty of resources that are pretty useless like shells or ink. Why not to use them in alchemy? Potions could influence many aspects of game, not only pet stats but also temporary change of their genes (so some potions would be reserved only for species with specified genes). Anyway, the potion-making shouldn’t be too simple. It might be interesting when recipes change month after somebody discovers specified recipe or after 3 months if nobody has discovered it yet. These changes exist, because the position of planets, the energy flow changes etc. are very important in alchemy and influence resources’ properties.

The power of potion should depend on crafting pet’s stats (I’m for intuition, because this stat is not influenced by genes), a pet’s specie (changes after a month, so there wouldn’t be an universal potion-maker) heritage (both, degeneration or hero should have positive or negative influences related to month) and quantities of resources.

To craft a potion player should
a) build a proper building
b) pick out 3, 4 or 5 resources and choose their quantities and proportions
c) pick on pet with proper heritage and specie what will make your potion stronger
d) start to pray
e) click craft

If player chooses well proportions and resources he or she will receive recipe which can write and sell to others (maybe to do so you need another schemes or blueprints from which you remove an old formula and write new?).

Player can also send 50 lvl pet to work for her or him in alchemist’s lab and receive a random potion recipe.

Another ideas of potions:

-          Enchanting golems so they can live longer or produce more

-          Healing, when you take this potion before battle it can restore energy point after lost battle

-          Energizing, when you take this potion before battle it can restore energy point after won battle

-          Midas, when your pet lvls up after drinking this potion you receive random resources

Do you have your own?

2.       Beast Temple. Why not allow another players to send there their pets to fight with these exploring islands? If you build your own temple and send a pet magicians and monks using some special mediums can turn them into wild beasts for a long time and send to temples on islands. The longer pet is there the longer is inactive after taking him back from temple (in the temple it’s getting wild). The longer beast stays undefeated the better award obtains its keeper. When the beast’s energy bar is 0 but pet is still undefeated it stays in temple and waits for another energy point, if it loses and has 0 on energy bar it gets back to keeper.  Gryphons can use gladiator bar. 

Both players should get mail about his or her enemy. It could be interesting for both.

If there are no beasts from players’ pet the system generate them as it is done now