Here's how I see it.
I have a little brother, see? He's in that 'surly teenager' stage, and he and his friends cause a lot of trouble. Sometimes what he does makes me mad because he can be pretty mean. But I still care about that lunkhead. No amount of meanness can change that. After all, it's not like we can stop being siblings. That bond is always there, no matter what happens.
In all the situations I know about, siblings usually don't want to hurt each other. I know that's the case for me. If it ever came to me having to fight him, that would be very hard for me. I doubt I would be able to do it. No matter what my brother does, I could NEVER EVER hurt him. But if it came down to that, I know I would hold back. Intentional or not, I would hold back.
And that is what I believe the situation is. Optimus Prime, intentionally or not, is holding back while fighting Megatron. He still cares about his brother.
So it breaks down like THIS...
Somebody who's holding back and gives a rat's patoot about his enemy versus somebody who ISN'T holding back and DOESN'T give a rat's patoot about his enemy.
Who do you THINK is gonna end up kicking skid-plate?
Life can be pretty sweet when your alt-mode is a B-2 Stealth Bomber.
And for those of you who are wondering... I'M A GIRL!
I'm not prejudiced; I hate everyone equally.