I found this vid done by Game theory a little while back. Don't know if you saw this one Flame, but it's definitely interesting and paint's both Dr. Wily and Dr. Light in a different...light. It also goes back to that discussion we had near the start of this thread.
Game Theory: Who is Mega Man's TRUE Villain?
Ive seen that. It bugs me though because it's wrong on so many levels.
First of all, we have no actual indication of Wily's nationality. Sure, Albert is a German name. Wily though? Not so sure... And thats hardly an argument to base anything on, even if it is meant for laughs.
Second- Light is not responsible for "every robot master". He made 6, then another 8 later on. That's it. After that, people just followed his example.
Also, Wily? Not a skilled programmer? what? It's arguable that Wily is actually more intelligent and actually more genius than Light. One only has to look at X and Zero to see that. X is Light's magnum Opus, but Zero is no slouch either. Zero and X are equal in terms of power, (post X1) With their legitimate fight in X5, resulted in a draw.  Wily also created the Viruses Roboenza and the Sigma Virus, from studying alien technology.
Also, the MM9 robots DID choose to help Wily. But this is being misinterpreted. They did NOT agree to help him take over the world. he said they would be useful to him, so they followed him. When he repaired them, he reprogrammed them to attack Humanity, just like he did in 1. they didnt CHOOSE to let him reprogram them.
The example of the autonomous gun turret is flawed also.
Dr Light's research in robotics allow robots to be able to tell right from wrong based on their programming. Sure they can be reprogrammed. But So can Humans. Ever hear of brainwashing? Light's robots, and most robots in that world, would never choose to harm a human. 
It's not untill the X series that we get robots who really CAN choose to hurt a Human "just because". And by then it's not Light's fault, but Cain, for mass producing them without thinking of the risks. (and not following the model perfectly)
Also by suggesting that without autonomous robots, Wily wouldn't have happened, let's consider the following:
Wily does not exclusively use free thinking autonomous robots. The robot stage enemies in Mega Man games are NOT free willed robots. they are very little different than any robot we have today who just follows their program to the letter without a soul. 
As for Letting Protoman get away, well, we don't know that he never searched. That's an assumption.
Also, he still programmed him. for all their free will, Rock and protoman are bound by their programming. Rock was programmed to be a good person, so he is one. So was protoman. The difference being he's only a bit more independent. Sure, he helped Wily in 3, but only out of gratitude for saving his life. He still betrayed him in 4, and after that, fought against him just like Mega Man does.