I SAW A THEORY OF THEM SAYING SENTINEL PRIME COULD'VE BECOME NEMESIS PRIME! honestly i'd rather Nova Prime appeared and did so but..eh..
Well, Optimus did shoot his brain at nearly point blank so I think it was unable to be "turned on". And yes I know Megs had an axe in his head but.. idk plot reasons
The OP betrays SO MANY misunderstandings. No one at KSI was INTENTIONALLY using Megatron's brain for functionality and/or design purposes. They harvested knowledge from the brains of Megatron AND Sentinel to crack the code of Transformium and make their own robots. Megatron's mind guided that process and asserted itself in the bodies KSI built under his command. That's why it wouldn't have mattered WHO the blueprint was for KSI's would-be Optimus-clone. MEGATRON WAS CORRUPTING THE SYSTEM TO MAKE HIS NEW BODY NO MATTER WHAT THE PROGRAM INTENDED. It's pretty straightforward.