Presumably if you do the minuteman ending, you only kill the Institute, right? Though, I'm not certain what I need to do to kick that ending off. I've been avoiding it so far, just exploring the wasteland, but I've been doing railroad quests so I kill synths, just not unless I have to. The Institute still hasn't excommunicated me. I guess I could go back to the institute and refuse to cooperate, in which case Sean would probably excommunicate me and then it would be on?

Yes, you can start that quest at any time just by turning the Institute hostile, but doing so before doing other faction quests will glitch your games or make you miss out on certain contend. Some people reported that complete the Minutemen ending without doing Blind Betrayal will make Danse unavailable and you will definitely not getting the best companion perk from him. As long as you are not hostile to any group and do the Minutemen ending, all 3 factions will be friendly.

There's no way I could destroy the Prydwen and blow up

This. There's no way I could blow up the cat. I've turned Abernathy Farm into a fortress to protect their cat! Junk Walls and turrets galore. If I could build a catnip bar I would. I just hope the food and drink vendor supplies kitty with his 'nip.

Battlebloodmage,

I'm with you, I detest the RR and I try to draw the quest to destroy them out, so I can relish each kill. I find them so vile, that they force me to admit that their are some things I just can't roleplay.

This.

Killing innocents for the sake of a bunch of looney-toonies doesn't sit right with me.

Killing a bunch of looney-toonies to protect your people? Now that is satisfying.

I blame the BoS for bringing little children on the Prydwen when being a soldier hell bent on war like the BoS is garrunteed to be fatal. Who gave the ok for children to be deployed into battle? lol dumb move.

Training, there are missions where you escort them to fight mutated creatures so they could learn from observing. Regardless, you could blame the BoS, but the children themselves are innocent, they've no saying about being brought to the Commonwealth.

It's obviously a matter of opinion, but I see this as the 'best' ending purely in the sense that it leaves you with more radiant quest opportunities after completing the main quest. With the Minutemen, BoS, and Railroad alive and at relative peace, you have quite a few more options for radiant quests than you would with just 2 factions.