I don't think Fate should change sides. That is way over done in so many franchises. Let him just be bad! I am pretty sure he is not the bad guy boss. Ken is saving that for later. The main boss in the series should be big and scary. Someone even Eva is afraid of. Ooooh, maybe her "father"? O_O (Or something!)
Fate is just bad. He may not even believe in the boss's plans/dreams. But he likes challenges like Negi (Son of the Thousand Master.). It's fun and exciting for him. Life is boring to him. He could never be a good guy/hero. He needs things like the current storyline to keep him interested. But he is bad.
I want to see this fully play out. Fate vs. Negi always no matter what. Even if everything falls apart and Fate has nothing to gain he should blindly strive to fight Negi to the very end. Give him one of those Metal Gear deaths/endings where he thanks Negi for being the greatest foe he ever faced. That for a time he had never felt so alive in his long life. He actually thanks Negi as he dies. Now that is the way to go.
I am sick of series villains turning over a new leaf and now in the new series they're heroes. All of their past deeds seemingly forgotten as water under the bridge. It happens way too often now days. Just let a bad guy be a bad guy!
Mahou Sensei Negima Forever!