Oki, I know you plan to add in some sort of avatar tree, I if possible I was thinking for the branches if not branches for a diff type of tree; healer, archery, warrior, mage, etc. and when your in battle your character has a giant mana bar at the top of the page or something. When your pets battle the bar fills, and the tree is for special techniques only, so when your bar reaches a certain amount it consumes that amount if you want to use it to do a special ability, ex: heal all pets 10% cost 25% of your mana bar or something. This way instead of saying your character participated in battle, your character DID participate.
Another couple of ideas; which prob may have a good chance of coming to fruit, guilds, a special guild forum, and inviting characters to guilds. Maybe this can be apart of the tree to or something else entirely different; allowing people to increase their levels in certain categories. ex: Fighter/trainer(someone who battles), breeder, healer, merchant, artist, etc. Basically jobs. Guilds can be built off these, say a fighter guild, and characters can make their own and name them, so there can be multiple fighter guilds. Maybe they could cost gold to create so as to not overly create guilds and obviously a way to disband the guild or have control of it. just typing this out makes me excited lol.

lol noticed, your post was a bit hard to read because it seemed to run together. I do get what you are saying though.
Having a character with their own element to aid in the battle would be great. More or less any spells that could be cast would benefit your pets but requires a mana gauge to be filled (probably a lot slower than your party's). Like the light for healing or cast a dark spell to drain the health from the enemy into one of your pets randomly.

As for the guilds I would suggest that it require quite a bit of gold, like 50k or so to create one. Maybe a special crafting section being placed into each guild depending on how it goes. The guilds can have specializations with bonuses that work throughout the game maybe? Like a breeders guild that could boost the chances of an offspring holding a gene or mutation that is not guaranteed (Visible x Carried or Carried x Carried).

The fighters guild maybe having a fighting boost to the party's pets? Mage guild to boost spells? It has a lot of possibilities to it.

Also to increase the guilds abilities require a fee to unlock a special skill. The members can donate whatever they like be it 1g or 1000g and that money goes to improving the guild with the money going into a special bank that can only be used towards the guild and can not be returned.

These are a few ideas that I've seen in other games that have helped a lot as long as the guild participates. That and the fees insure that members are participating instead of just mooching off the other's hard work.

The building for this could easily be set up in one of the towns. Kinda how they did the arena in Astryl's Vale.

@Lunesca,
yea, you seem to get what i'm saying, sry I tried to make it not so confusing. But your add in for the guild sounds cool too I like the idea of special boost.