Is there any way to peacefully resolve some of these, particularly the Brotherhood? I have Veronica with me and I did the quests for Elder McNamara. I did not do the second set of quests for him to join the Brotherhood myself.

Since Mr. Houses only option with the Brotherhood seems to be to destroy them one way or another I don't see how I can get Veronica to stay with me. I am in the process of finishing her quests and I plan on having her leave the Brotherhood and work with the Followers. But even still, she may have issues with me killing all the Brother off.

I do plan on doing the House quests this time. I did NCR last time.

If you do more quests for the BoS before destroying them, you won't be vilified(only soft-hearted devil) and Veronica can stay. At least that's what the wiki says.

Edit: It also says you can wipe out the bunker without blowing it up by hacking the turrets and using sneak kills. This will result in no infamy.

I never understood the kill with no witness options in FO:NV. In Skyrim if you kill someone and there are witnesses around, you basically get a bounty on your head. If you immediately kill everyone that saw you, the bounty is removed (as there are no longer any witnesses). Seems odd that I can go into the bunker by myself, kill every single person, and still leave with a huge hit on my Brotherhood rep. I do believe the Skyrim way makes more sense.

I'll be honest, just going through the endings in this game on the wiki I have to wonder if there is a good ending in this game. I'm actually considering doing what I had done with many Skyrim RP's and this is to just not do the MQ at all. Befriend who I want to, do the quests I want to, and then just retire the character. Starting to make a lot more sense now.

If you must, you can try this mod: http://newvegas.nexusmods.com/mods/37729/?

Well that's an interesting mod. I guess I'm not the only one that didn't like Mr. Houses only options for the Brotherhood. Course being who he is and how he is living, and what the Brotherhood does about tech, I guess I could see why. My main concerns were really for Veronica, as I've gotten attached to her. I wonder what that mod does to the ending slides?

Thanks for the link. But I guess by it's being there that what I was looking for in the vanilla game just doesn't exist.

You need to do more for the BoS like doing McNamara's quest to get liked by the BoS so Veronica won't leave. Furthermore, don't destroy the BoS while Veronica is with you since she will automatically leave if you go and kill BoS members.