Here's my thoughts on Bio's. It's nothing more then ideas and brainstorming. I don't know how long you plan on working on them and some of my idea's could take up more of your time then you wish to devote to Bio-engineering. Take what appeals to you and I invite everyone to discuss the topic.
Bio-Pets:
1: First major change I'd like to see is them brought in line with other pets and become levelable. This would give control to the owner on things they feel need to be improved. This also includes stat loss (which I know is on your list of things too look at) but only if pet repair becomes more accessible - currently you would have a hard time repairing any major damage since Goo's are uncommon; especially since you would need large quantities of them. Maybe have Vet and Animal Lore increase how many points are repaired if you don't want to increase the number of Goo's?
2: Their special attacks need to use less stamina - less stamina means less attacking which means less damage. In most cases the trade off isn't worth it. I'd also like to see their abilities split into an active (Comet attack, Ice blast, ect) and a passive (Immunity to poison, Enhanced hit points, Extra tough armor, Immunity to mortal strike, Quickened stamina regeneration) with the active being offensive in nature while the passive being defensive. I'd say 5-6 in each category would provide a large enough selection to make a variety of usable pets.
3: Currently they do physical damage; it would make them more desirable if we could sample a fire based creature for example so that a portion of their damage became fire. Cold based creature for cold, and so on for the other kinds of damage. It would also give a reason for having more then 1 Bio pet - right now it's one pet for all situations. Bring the right tool for the right job type of thing.
4: Control slots need to be standard. In my opinion they should have the same power level (maybe slightly above) as a AFS so as to not overshadow animal breeding and Taming. They should cost the same in pet slots - make it 3 and call it a day. I've never had anyone request a lower pet slot Bio - they want big beefy tanks or extra damage. Micro managing anywhere from 1 to 10 1k hp pets that don't do any more damage then a regular pet (alright maybe slightly higher) is not a popular playstyle. I maybe wrong on this one so if someone disagrees please speak up.
5: An interesting concept would be to have pet types such as a healer pet, tank pet, mage pet, druid pet, dexer pet, swords pet, ect; similar to the donation pets but on a smaller scale (they don't heal for as much or do as much damage). This one is really dependent on how much time you want to invest in pet types.
Sampling DNA:
1: I'd like to see the mimic broken into Mimic (the model type), then Offensive power and Defensive power (or whatever you decide to go with). So you would need 6 types of DNA to make a pet. I'm comfortable with how Prowess, Environment, and Mental are obtained and the risks involved. If you went with different pet types then each kind of sample could make two or three kinds of pets.
2: Additional information from the advanced pet wand such as "this would make a good a good fire based pet" or "this creature has very strong druid magic". Knowing what to sample would go a long way to making it worthwhile to try and sample a mob instead of praying and hoping you get a good one.
3: Sampling a mob should give a sample related to the mob type. Counter heal should come from any healing mob, Ice blast should come from ice based mobs ect. - to me it's just common sense (I do not know why the original designers didn't go with that model).
Storage:
1: Bio's can't be shrunk and it would be a nice addition if they could be (or if the pet summoning ball was craftable with rare drops from high end mobs or BODs). Dragging a Bio through some places is a mess waiting to happen.
2: DNA Vials (both the single and the sets) and Samples tend to build up and having a way to recycle them or store them would make life easier. Kane said it's "on the list" so this isn't as a big of a concern to me.
If I think of more I'll add it but it's just some idea's to toss around.