The plasma pistol should be your secondary weapon without a doubt, some sections will take multiple times and as you say the AI isn't much help, they cant die but by te same token they are not aggressive either.
As for the armour abilities, this is probably obvous to you but anything outside of the drop shield, sprint & maybe armour lock is really not worth having outside of the specific situations. Even against the enemy AI hologram is pretty limited.
The mission where you are paired with Gorge on the cruiser instantly springs to mind when thinking of the hardest section, it's surprisingly one instance where the AI comes in good use. You are rushed by about 8 or so Elites but if you remain around the edges they have a habit of being drawn to Gorge who constantly runs around the centre of the map.
Good luck if you plan to stick at it, I know how much of a frustrating experience it can be.