No spoilers here, I promise (and let's keep it that way).

BGS has a long standing tradition of amazing environmental storytelling, memorable side quests, and lackluster (or at least ho-hum) main quests. I do feel that Fo4 bunks that tradition and delivers a pretty good main story. However, there's one thing about it that bugs me to no end:

There's a massive lack of interaction between you as well as the main factions, excluding the Minutemen, and the people of the Commonwealth. Sure, the BoS want you to force settlements to support the BoS, and the RR occasionally wants a settlement to act as a safehouse, but that's about it. You can do quests for different people and places, but there's no growth in that relationship. You do the quest and that's it.

Take Diamond City: I do all that work for them and the people of Diamond City still want me to buy a deed so I can settle there? WTH?

This is something that New Vegas handled really well. Different factions could be convinced to aide you in the final battle for the Hover Dam. Not all factions would support a given side.

This idea is one that could warrant massive changes that will never happen because the game is already out. We're not going to be able to convince Goodneighbor to support the Railroad and fight with them because BGS likely won't add it and it's likely something above what modders can do. For most purposes, this is really just a study in lessons learned and what could have been. However, there are smaller changes that can be made to make it feel like you're at least building a relationship with the people of the Commonwealth.

Let's use Diamond City as an example:

It's a locale with a ton of quests available. It'd be great that at some point in helping them, the market stores get together and decide to give you a discount. Later on, they could pitch in and sponsor your house there. Finally, you would be able to send provisioners from your settlements to Diamond City which would increase the chance that a given merchant at Diamond City will carry a legendary item.

Maybe the Atom Cats can be convinced to patrol nearby settlements, increasing their defense without you needing to build turrets or outposts.

Small things like this could make it seem that I'm actually helping people and making the world a better place. Sure, mods can fix this, but I hope it ends up being something that BGS can learn from. Beyond this, it'd be great too if shady places were recruit-able too, like the Combat Zone or the Triggermen. Why are these places automatically hostile? It's a massive opportunity that was squandered.