I finished the main story line of Fallout 4 last night and its been playing on my mind since. Maybe I’m getting old but but the ending is nagging at me. I think the ending it's too black & white, it left me a little disappointed after putting the time into finish the main story line.
The ending was basically which two of the 3 factions do you want to kill off, (I'm discounting the Minutemen as they are fairly benign by the end of the main story). I’d liked to have seen an ending where you had the choice not to just wiped everyone out, but take the best from all the factions and create a new hybrid with you at the helm.
I’ll outline below how I would have liked to see it end.
Being the new Father of the institute you could have changed its direction. You'd probably have to do some missions to take out those who would oppose you and keep your access to the relay open.
The end game could be Father sending the last of the Coursers to assassinate you when you're in one of your settlements, actually make use of what you have constructed, maybe the minutemen could help out a bit? Fending off the attack you head back to the Institute to find Shaun on his death bed, the last dialog would be along the lines of:
1, You say what he is doing is wrong, he is no better than anyone else in the wasteland and finish him off yourself,
2, He blames you for the downfall of humanity and passes away , along the lines of what actually happens if you don't pick the institute ending.
3, (charisma) you convince him what you are doing is for the best, forgive him for what he has done and he passes away.
This could allow you to bring the Railroad into the institute and work to give the Synths a choice if they wanted to stay and work at the institute or leave to live in the commonwealth and beyond. If they chose to leave then the Railroad would continue to work help them against the dangers they face with the institute’s help. Those who stay are treated as equals and continue to work and keep the institute running.
For the BoS it seemed to me that it was just Maxon who was pushing the destruction of all non-humans and non-human sympathisers. Perhaps a shoot out at the Airport including having to take down Liberty Prime could be a good way to finish him off. From there you and a host of Synths teleport to the Prydwen and give Paladin Dance a choice (seems fitting he takes charge uponr Maxon’s death):
1, (charisma) Join forces,
2, Leave the commonwealth, the Prydwen fly’s off the map.
3, Die, shoot out on the Prydwen which is then destroyed.
If you were able to get the join forces option your reward could be Proctor Ingram, working with the Institute scientists, to make you some Institute Power Armour. Not just a painted set of X-01 armour but something completely new. Seems like there is a lot of scope for new Weapon’s and Armour, Institute gattling lasers and such.
This ending could lead into some future expansion packs for Fo4 with other BoS factions taking a dislike to what you’ve done and coming after you maybe a kind of BoS “Civil War” expansion??
?If you picked either of the other endings BoS/Railroad then there would have to be some backstory made up about survivors of the institute teaming up with defecting BoS members to make the third faction.
Anyway thats getting a bit ahead of myself, just think there was an opportunity to end the main story in a more satisfying way and allow for some continued game play as a "new" faction.