Won't be too hard to code, at least, i think so 
The fishing machine will use energy, and must be placed above water. It will automatically be shot out of the top of the fishing machines cube. Because i am currently playing IC using tekkit (the other mods finish it) it would be a great addition;
Think about this circuit:
A nuclear reactor, generating TONS of energy, which is transported to a big field with 20 fishing machines. they will use a pretty big amount of energy, but the reactor should do ;D Now the transport pipes of Build Craft will transport the raw fish to the electrical furnaces. Which will cook them using some of the energy of the reactor 
Now they will be transported to a chest, infinite cooked fish 
What d'ya think?