I'm not sure if you did this, but in my experience, you need to score every single fold line, even if the "fold" will be relatively flat. It really allows the paper to shape itself however it needs to according to the glued seams. Plus it's easier to shape it later once it's all together. I use a blue or red fine ball point pen and a ruler. That way it's easy to see where I've missed and it differentiates between the folds and cuts. Don't use black!
Also, don't be afraid to add internal support and bracing with card. You can even use sticks inside if you need to bump out the shape (on the face, for instance). Once you harden it you'll remove the internal bracing. Remember that nobody will ever see the inside so you can do whatever you want. the outside shape is what you need to get right.
I've also had paper models (helmets most especially) look like poo until every single piece is in place and it pulls it all together. You may find that you'll have to add the detail pieces such as lenses just to help it come into shape, and then cut them out later. I've never done a Stormtrooper so I can only speak generally.
-Rog