First time I played it, I accidentally walked right past the room ED-E was in without seeing it, so he ended up dismantled lol. But I got the Lonesome Road perk, and since I rarely traveled with companions, I only felt bad about it for like a minute.
As for Ulysses... By the time I got to that point, I was so high leveled that I sniped him with the upgraded anti-material rifle. With all the stealth bonuses, he exploded before I had even entered the room proper (I was in that small room right before it). So didn't even talk with him ha. Then I nuked both sides, since I was doing Wild Card and was already on bad terms with everyone.
So basically, I ended up taking pretty much the most psychotic routes for every decision, accidentally or otherwise.