Not going to touch on the rest, but its heavily implied that the Prydwen's reactor came from Rivet City... and the BoS didn't ask politely.
Surge? You mean FEV? Because according to idle chatter from Super Mutants out in the Wasteland they either ran out or are running low on it. The BoS could eventually simply outlast them as a result.
And don't get me started on the FO4 factions. What I would have done is have the Minutemen be the player's main faction, operating out of Concord after being broken in battle against the Gunners, and you work with them setting up outposts to rebuild and retake the Commonwealth settlement by settlement, your job taking you all sorts of places that let you dig up info on who took Shaun and why. You eventually find out it was the Institute, and then after dealing with Kellogg and making contact with the BoS and Railroad, the Institute takes out your boss in a hit and you get the top spot because plot reasons. You can then pick and choose between the idealism of the Railroad or the pragmatism of the BoS when it comes to dealing with the Synths and Institute. And since the Gunners are being employed and equipped by the Institute as a direct action unit that can be used in ways the synths can't, its personal for the Minutemen. So picking Railroad or BoS has other effects regarding story, the BoS acting as heavy hitters if you side with them and fighting directly against the Gunners with the Minutemen stuck dealing with synth black ops units, both overt and covert in a shadow conflict they really don't like or want, but if you side with the Railroad the Minutemen are forced to go up against the Gunners themselves in what will inevitably be a lot bloodier than if the BoS handled it, but the Railroad are much better at engaging the Institute in shadow war.
No, I mean the infinite amount of Surge Soda they have in the Vault that breaks canon and causes NMA to freak out.
My issue with the Bethesda Fallout is that they very will do bullshit like have a heavily armed group appear in a region and never do the fun stuff that better games have done. Raiders are just Raiders, they're not given any background. They exist as anarchists who hate people who do anything, crazy cults exist that are just that. New Vegas had the fiends who literally are a bunch of violent drug addicts chasing highs, Powder Gangers who are convicts running from the law that will kill them on sight, and other gangs that ran to Vegas to escape the expanding influence of the NCR. Some of these groups are just callbacks to Fallout 1 and 2 or literally drug addicts who will rob you for more crack money.
My big issues with Fallout 4 beyond lack of RPG elements:
1. The Gunners are not even anything beyond raiders with combat armor. You never even talk to them, they might as well be Super Mutants. They aren't an actual faction, they exist to shoot at the character no matter who you ally with.
2. Bethesda sets up locals being upset about the BoS not actually fucking learning about the locals or the area, but never actually has groups hating them for fucking up. 'Raiders' being pissed off locals who take pot shots at BoS and fuck over their infrastructure would be a fun mix.
3. Locals are have no actual control of the area they live in. They are at the mercy of the larger factions rather than factions of their own. The Minutemen do not exist, it's one guy. If the Minutemen were a militia group formed after settlements got destroyed by the Institute that'd be neat. They'd be the Knights of Malta in fallout.
4. You can not get off the rails. NPC's are immortal and YOU WILL ENJOY THE SHITTY DIALOGUE THAT EMIL HAS WRITTEN! YOU WILL ENJOY THE LACK OF VARIETY OF WEAPONS! YOU WILL WASTE HOURS BEFORE REALIZING BASE BUILDING IS SHIT! AND YOU WILL LOVE TODD!
I don't think Fallout 4's story could have been saved. It's a really long side quest blown up and then you're given the shitty settlement building mechanic to waste your time with. 76 is honestly worse because it gives illusions of control. The weapons have no real difference in them, the whole Borderlands-esque legendary weapons is terrible. The design of them sucks too. The perk cards and lack of skills drags the series down. I have watched one Fallout youtuber who defends 4 and 76 and it hurts.
76 does have a quest where a BoS Paladin fucks up tremendously and kills a town because of her shitty judgement. I tried killing her so many times because she was just sanctimonious about trying to help people out of guilt, hiding her fuck-up, and browbeating the guy who's trying to deal with her fuck-ups. The other guy is not any better, but he's tolerable by comparison.