After playing through the game numerous times.  What has really bugged me about the story is at the start of the game.  So you control some dude with the suit on and the evil guy takes control of the suit rendering him helpless.  
 
But when you go around their base and collect their suit for some reason they are powerless to flip the same switch and lock you down.  This made no sense to me and since the story is so bare bones and ridiculous to begin with this just added a cherry to that nonsense.  
 
Oh btw great game this just really bugs me! Is there something I'm missing?

Nah, the story is just an excuse to kill dudes and collect items.

You need to read the book "Empire". It's all explained there.

maybe that was the main "villain"s suit? would you like it if you had an off switch in YOUR suit if you were the boss? 
no

I just took it as the suit you got was like a new prototype, so they hadn't implemented a shutdown switch in it yet.