Well, I am a physics professor who shoots, and the answer can be found in the internal ballistics equations, which no offense intended, are too complex for the average person to understand, involving first and second order differential equations.
The short answer is your premise for your reasoning is wrong, and you are leaving out important things like the amount and speed of the powder gas(think rocket motor), the difference between peak pressure and area under the pressure curve (what actually does the work of moving the bullet), and expansion ratio of the cartridges (important to efficiency). Also, your statement of Newton's Second law is just wrong, as the equal and opposite are
forces, not energy.
Your question is about like asking why two cars traveling the same speed don't get the same gas mileage, and the short answer is the same: there's more to it than that.
Here's simplified articles that may help with the concepts.
Recoil - Wikipedia, the free encyclopedia
Physics of firearms - The Gun Wiki