I just thought of something...
No-one is supposed to know the Agents are animals.
The agency most likely chose animals because no-one would suspect them of being agents.
Yet crime fighting animals would actually draw more attention...
So I'm assuming the Government is covering the whole "Animal Agent" thing up.
Here's what I would do if I was doofensmirtz :D
I would fight Perry like normal but hide a secret camera. (Despite he's monitored at all times) and film the entire fight, then put it on the internet or send it to a news station.
The press would get word of a martial arts fighting Platypus and the whole entire agency would be revealed to the world.
Perry would no longer have a secret identity and O.W.A.C.A would probably have to start over with another concept of fighting crime meaning no more Perry to fight him...
But since Doofensmirtz isn't very smart, and he enjoys fighting Perry that would never happen.
And here's a question.
The training of Animals to fight crime... would PETA be against that? (Putting them in harm) or approve? (Animal Empowerment)
I know I'm taking all this too literally for a show that really doesn't make much sense but I was just saying my thoughts.