(SPOILER)I read through a walkthrough and it looks like killing Mr. House too early might cut off a quest line, even if you get control of the Securitrons.
So, when I killed Mr. House to save the wastes, I unwittingly ended up helping Caesar. And then killing Caesar to save the wastes put Lanius into power. I got the worst ending by doing the things I thought were best. It's a heavy-ass game.