I disagree. They should have nailed the balance between them this time around. Prime should have been owning 3 decepticons and when he would be finished with them, Megatron should appear and they would fight. And if you ask me, they should be equal, or maybe Megatron having a slight edge since the decepticons were born to be fighters.
Prime owning Megatron and 2 of the strongest Decepticons at the same time is just bad writing. They were clearly trying to make up for the last scene of TF1 but they nerfed Megatron very badly.
That makes sense, but it also needs to be done right. If Prime used his new guns to kill him, then his weakness is just getting fired upon. If Prime used the Matrix of leadership, or something else that is exclusive to him, then yeah, only a Prime can kill the Fallen.
Which again poses the question: How come the original 12 Primes (who are supposed to be gods) couldnt kill him, but Optimus alone can?