So I use a 3rd party controller with no six axis and my flashlight is acting crazy and I can't shake the controller to fix it.... Is there a way around this? And also is there anything else that recuires six axis in this game?

There is no part in The Last of Us where you have to use the sixaxis feature, I think.

The game asks to shake the controller every once in a while, but I still haven't figured out what it actually does. :p

But my flashlight is flickering and it tells me to shake the controller...

That never happened to me.

Weird.

Theres a part that makes you tilt the controller, I honestly have no clue in hell what it does though.

Did a little research and I guess I was wrong. You can turn the light on/off as much as you want but it won't recharge without the SixAxis. It will still kinda work but it will flicker heavily.

In the bottom left it shows a controller shaking, and when I shake the controller it goes away. Never noticed any difference though before and after shaking the controller. 

Let's ask the Naughty Dog expert Aldro. :p

Wtf... Lol

buy a first party controller, problem solve =)