I've hated the inner box that the game came in so I went to my local dollar store. The had snap enclosures of two sizes that I thought would work. I bought them home and was pleasantly surprised. After I got the situated in the box, I labeled evyerthing. This was the outcome.
Box with all components
Components and small boards
Components, small boards, and large board
The only drawback...the lid almost fits.
Mechs and characters
The black faction in a small container
The sleeved cards fit perfectly
Pretty much everything else fits in here
Here is an Amazon link to the exact containers I got. They are more expensive on Amazon than at the dollar store (3-pack for a dollar). YMMV.