[SixOfSpades]

Your characters don't have to actually be standing on top of items in order to pick them up--they have a bit of "reach" and can access things a couple of feet away. The next time you kill a bunch of enemies right next to each other (which shouldn't be long), have your loot-collector stand on 1 item pile, and give them a bunch of Plate Mails, to make them Encumbered: Can not move. Then, tell them to grab items from nearby corpses. Even though they can't move themselves, they can still reach the loot.

Sometimes items are still a little bit further away, but you can still get the gear: A good example of this is in the Sahuagin City, when you kill a Sahuaging that's in the water, but very close to shore. You can position your character as close to the loot as you can, and tell him to grab it. It'll take him a few seconds, but he should be able to reach over the barrier and nab that loot.

But you sound like the Master Brain has dropped his gems closer to the middle of the Brain-thing than the edge, and if so, that must be a bug. Usually he drops the loot much closer to the edge of his tank, and I've never had a problem getting it, in the manner I've described in my second paragraph. I get the idea that BioWare anticipated gamers potentially having trouble obtaining the loot, as the only quest-specific item that the Elder Brain drops (his blood) is automatically transferred to your Inventory, whereas the blood dropped by the 2 alternative targets is picked up off the floor just like everything else.