So I completed the game, and not hastily mind you. I have well over 60+ hrs.
To me, and the issues I have ran into are really disappointing, and seems to not have been carefully planned out by the game creators.
Let's start with as much info, and as little amount of words I can, to explain.

Throughout the game I have done a ton of stuff for all the main factions ; Brotherhood, Minutemen, Railroad, and the Institute.
All of them, I have completed their quest chains up until the better point of an expected completion of the main story.. Decision time, Decision time has arrived. And what a damn, confusing, and unsatisfying end I have arrived at.
Ultimately I have ended the story siding with the minutemen, but have done soo much for the Brotherhood; side repeatable quests, sub-main quests and the building of the Prime robot. At a certain point I was unable to associate with any Brotherhood's important characters. Elder Max won't even speak with me anymore. There is a Giant robot of annihilation just standing there.
Now I understand that my choice to the Minutemen reflected upon this incident with the Brotherhood, but I very much expected them to continue on without me. I Expected to see that robot in action reguardless of my choices. I expected to see the Brotherhood continue their mission against the Railroad and the Institute, behind the scenes. I expected to meet them in the confrontation between Myself and my Minutemen, against and inside the institute. I expected SOME form of follow up, or interaction with the Brotherhood, but there is zilch.. They stand around like a forgotten plan, ignoring the remaining Synths ( The Railroad ). To me that is lame.

The Railroad.. Excepted the fact that I chose the Minutemen and supported me to an extent. They wanted me to talk with Preston about figuring out how to get back into the institute.. I was unable to talk to Preston about the Railroads assistance in helping to penetrate and take out the Institute, which seemed to be caused by me giving the holotape to Sturges, though the quest to do so had the marker still on Preston. At least after the destruction of the Institute, I was able to go to the Railroad HQ and be thanked by Desdemona. Desdemona spoke about the future of the Synths, the Brotherhoods objectives and a hope for the future.

To me, this is an incomplete ending, even if the ultimate goal was to stop the institute. Why are the Brotherhood not continuing their goal in extinguishing the Railroad and other Synths. Why am I still able to play the game, just to roam freely, do repeatable quests that lead nowhere, search for more bobble heads, and trophy completions, and not still witness the Brotherhood and Railroad in action, or at least associate to a verbal conclusion to why the Brotherhood have developed amnesia of any events or goals they were persuing? Must I really play another several hours, just to infiltrate the Institute with the Railroad, and then again with the Brotherhood, just to see a different ending? That could take another 60 hrs, and finding a previous saved game to a point where I still have a choice, just as long. But even if I did this, would it not wield the same inconclusive conclusion?

Forming an alliance with the institute was my original plan after visiting there, but at some blind point in the game I made a moral choice for humanity and was never aloud back into the institute. Being a little upset and confused, I just said screw it and moved on. The Brotherhood blindly through me out after making me Paladin, by a quest I was doing, unaware of the outcome and never being told I was not allowed with the Brotherhood anymore, as well with the whole broken quest to team the Railroad with the Minutemen. Whoever you choose, everything and everyone seems to stop. I didn't like that very much.

I may play again just to see the ending with an alliance with the institute, but I can already predict that I become the new leader of the institute, just by seeing 'Father" sick in bed. I already know the Railroad will despise me, and the Brotherhood will banish me. ( though there are some things I am unsure of what will happen, so please don't tell me what, if you have stuck with the institute ).

To sum this all up, what happened to everything going on in the background? It all just stops.. No more stories. Have I missed something? Messed up somewhere?

Well, the Brotherhood is stopped in its tracks and doesn't honestly give a crap about the Railroad save as a means of getting to the Institute in order to destroy the Synths unimpeded.

With the Institute destroyed, 90% of all Synths are destroyed anyway and the rest is a mop up operation.

They've also been rendered utterly meaningless.

Sort of like after D-Day, the German government fell and was conquered.

Yeah, they can destroy the Railroad but that's a meaningless gesture at this point.

Remember, the Brotherhood thinks the Synths will take over the world if the Institute continues. The ones free and on the surface are no more dangerous than Super Mutants or Feral Ghouls now.

in the BoS ending of the game, you actually DO wipe out of the Railroad. same with the full railroad side, you wipe out of the BoS.

It is only the minutemen side that allows both to still be around.

Yeah, without the Five Leaders, the Railroad is a bunch of people who can't get in contact with one another.

Besides, there's no Synths left to liberate.

True enough I guess, when you put it this way. I must admit though, this is the very first game, out of many, many, many, games I have played, that had no " congratulations, you've done it!" with a 10 minute credit scene ending. It's just a small cut scene that explains to me that my efforts were for nothing, and that war will always be, and that I am a murderer of my own kin, and that the world is still a baron wasteland with less robot-like people. I truly hope that the 4 DLCs I've paid for add onto this abrupt ending. I am satisfied with the game and really Unsatisfied at the same time. I need more to this story! I want to visually see my efforts glorified, and with absolute, noticeable life changes for everything that I have done. A Transformation of the Commonwealth that I can be proud of! Right now I feel like a Vigilante without a reason to continue anything for the greater good. I am unpraised, Piper... Where are you?? You need to write more about me and my exploits! Commonwealth?? You can start rebuilding now, and not fear intervention of the institute replaced kin. Isn't that what you wanted? " Now hiring garbage men ". Expect lots of overtime. 10 caps/ hr. Bring your Rad suit.