Skeleton and Animation issues aside, I do like the idea and I am a bit of a sucker for fishing related things. My only issue would be to make it if this was used in some way for a rare version of a Hydra, rather than for the entire family, kind of like the MOP rares.
It is a lot of work however for just a rare, but maybe if they used the same system we currently have? Instead of having a "foot print" have a "fishing pool" (Pool of Panicked Fish?) as a marker to which one would need to flare into. But as you suggested, these pools could spawn in many waterways around the continents to avoid the camping issues of rares. Anyway, really like the core idea none the less
As for Hydra candidates, atm due to all of Wain and Noahs tireless work, all colours from both models have pretty much been accounted for and introduced quite some time ago, even though they are not tameable (yet
)and also that most people were not aware of all the model/colour changes. The only Hydra colour/model combo left that is now not in game is
HydraSkinBronze : was only available on Wavethrasher and Young Wavethrasher in Azshara (both removed). Hopefully some could be returned.
Anyways, just food for thought
.I know Blizzard hates the model of the hydras thus not making them pets so this idea would fix it hopefully. I got my idea from the unborn val'kyr and the pandaren rares. The hydra would come in 3 new looks/models. They would fit whatever blizzard feels would fit and be a rare(Maybe a 1-4 hour spawn). There will be 1 in eastern kingdoms, 1 in kalimdor, and 1 in outland. But each one will have many spawns on the continent. They would be like the pandaren rares where only hunters would see them....however you will find them in a hunter only fishing pool and fish them up and tame. It would sort of be like the spirits from sholazar basin where you would need to summon them but in a fun way. I think it would be cool to have 1 per continent. Maybe not northrend/pandaria because they don't have other hydras there. It would be a time consuming tame that would be a nice addition to rare pet finding. 
