I've been wondering the same thing about the rest of the community as well. What i'm doing isn't the most elegant solution but I set Trinity to quest mode so that it picks up and salvages everything and I made the item score requirements very high so maybe something totally awesome will get through all of the salvaging. Unfortunately I have no basis for understanding what the item scores are and I work during the day so I don't have time to figure that out right now. For now I will try to balance those item scores so that my stash doesn't fill with crap and I keep the maximum up-time while also trying to nab some excellent items. At least I will have lots of stuff to craft with at the end of the day and paragon levels.
As for sometimes ignoring blues and whites, I wouldn't worry too much right now because someday, after the loot has been optimized, we will look back at this moment and think... "Remember that time when the bot didn't pick up every single blue and white to salvage?" I'm sure just leaving it on overnight will net you plenty of neat new items and mats to play with. These are just my thoughts on how to handle looting right now. I hope that helped some.
