The Flight or Fight theory is something I ponder with all of my characters before I write them.
I wonder if my fellow writers consider this theory. I'm not just talking on a confrontation type of situation with limited consequential value. I mean in a life or death situation because I think in order to understand our characters we need to venture there with them (not necessarily in our stories but before we develop them).
Over the years I have seen people at that pure raw emotional level. And I learnt early that first impressions such as looks, build, age and sex of the subject isn't necessarily an accurate guage.
The thing is, given enough time - everyone will break down to pure raw emotion under certain circumstances. That animal instinct where we fight or flight.
So imagine your characters broken and at that raw emotion type level. What is their natural instinct? Do they fight or flight?
We need our MCs to have a vulnerability. But, we shouldn't just make it a 'cosmetic' vulnerability. We need to dig deep into our character's lives and start by figuring out what their raw emotions would be. Then give them a reason for those emotions either way.
I find starting with the raw emotion and building upon it doesn't 'cheat' the reader in the end. You know the feeling you get when you say 'I knew he/she was evil/good', that's because of the raw emotions you start with. After that you can twist and add to suit your needs for the story.
For me, this is truly understanding your character and allows you to build their personality upon it.