Baggins: Honestly I found the worst area is inside the Many, before you get to the brain. That small very tight canyon, no places to hide, and unlimited stream of tanks Rumblers and Psi Reavers. I ended up just like speed running through it, until I got into the main cave, killed the Psi Reaver brains, and then focused on the reaver projections, and tried to make my way back to the lake at the bottom in order to hid below the cliff where any remaining reavers couldn't reach me.
I had lots of gun ammo at that point, and grenades, so used them to take out the enemies. I always conserved inside the Von Braun. Since there weren't a lot of enemies to have to worry about so much in those areas, that I couldn't take out with crowbar of crystal shard.
I think the next time I play through I'll try for an OSA, rather than the Navy, and see how things turn out..
If you will playing OSA, best for that part is using invisibility and turn them against each other also by other psi skill (the one that makes any organic creature hostile to another).