Greetings. Very simply [EXOTIC_DOMESTIC] would be a new raw tag for application upon animals.
Exotic_domestic would be applied on nearly all mundane non-giant animals from non-savage areas as well as vermin (with a shortlist of animal excluded within those catagories based off entity usage [EVIL] for instance). Reason for the lack of giant animals being tagged in this way is that they would be harder to manage and unsustainable to ship out on wagons due to weight, and it makes a nice balancing act given that giant animals would be too great a powercreep. (why keep pigs when you can have giant boars which are directly better?) On top of not invalidating the elves magical ways to wrestle control of animals to be completely tame.
Typical pet values would stop this feature from being broken, and as a primary catch, all embarked EXOTIC DOMESTIC animals would arrive in a wild state within species separated cages (and all aquatic animals within green glass aquariums filled with precious water) meaning you would have to domesticate them yourself, on top of responsibilities of securing these animals in the first place.
For them to open up in the embark and market traders, players would have to domesticate, capture and sell off a pre-requisite breeding pair at a civilization animal knowledge value and individual animal training level (subterranean animals are easy to do for this reason but may be exempt from above ground and embark trading due to sub-terrain access rules making it only sustainable from merchants post-settlement)
Similarly to the real world, this would be the basis of the exotic pet trade, the domesticated animals are breeding stock for the mountain-home, and being unfamiliar with these animals they can't send reliably domesticated animals back to fortresses (AKA you) even with all 'the knowledge', that they gather up.
This new tag may prompt change on how animals are domesticated, allowing non-pet livestock to be domesticated if they fall under a [EXOTIC_DOMESTIC] tag, and the localised/civ wide catagorisation of how much dwarves know about animals so that even with a good understanding of a animal, it does not become a easy job to tame powerful grizzly bears to a easy domestic level with under-invested starter animal training dwarves.
For the purposes of adventuring, exotic animal totals in sites are restrained in cages or restraints. Releasing said animal in a public place may create a distraction.
As far as mechants are concerned, pets and exotic pets can be divided up into two trade good commodities for fluctuating prices and to stop large confusing lines on both embark and outpost liaison paperwork. Essentially you're buying a container full of bears on embark instead of domestic animals that arrive freely with you, live vermin may also be a additional food source (a container full of live river fish vermin for instance for instant processing)
Additionally wild animals obtained this way can wander off map to join the regional totals and wild animals can be bought directly for wild game reserves, conservation and introduction/reintroduction without affecting the current wild population spawns. Catching and selling sea serpents to the market may eventually turn up trumps in letting you buy a breeding pair later from merchants (with raw twiddling to enable EXOTIC_DOMESTIC and OCEAN PRODUCTS to enable serpents to be purchasable)
Additional Reading
[DOMESTIC] Tag changes Author - Cyroth (October 19, 2013)
As always feedback is always appreciated.