Fallout 4: What Can You Skip?

Not Joining Minutemen, Diamond City, and Other Avoidable Quests

This page contains some unavoidable spoilers, though I do not go into detail. It's mainly for people playing the game a second time, and many will with the new DLC coming. Fallout 4 is a very flexible game and will allow you to skip several things from the beginning on a first or second playthrough. This guide lists some of those quests you don't have to do, and how you can easily use the Settlements system without ever meeting the Minutemen.

Can you Skip the Minutemen and Still Use Settlements?
Simply never go to Concord, and you can completely skip the Minutemen and Preston Garvey's quests for a very long time if not forever. By going to various Settlements, you will get the same quests - Garvey is just directing you to new Settlements, while you can actually do these things on your own time. You should get the exact same quest you'd get from Preston Garvey if he directed you to the Settlement. Once you're done with that quest, the Settlment is then under your control and you can build as you please.

To take over a Settlement, simply click on the Workshop. This applies to Sanctuary as well. You do not need Quests from Preston Garvey to take control of that Settlement, though you may have to return there after having taken over another. The only one you likely need the Minutemen for is The Castle.

You need the Minutemen for things like Artillery, and they may be an option later in the game if you fall out of good standing with the Brotherhood/Institute/Railroad and want to finish the main story, but they really aren't tied to the Settlement system at all. You're free to explore, do side quests, and other things. In fact, you can skip other parts of the early game as well and advance past some of the steps that take you to Kellogg's house. Things change later and become very non-linear once the Brotherhood arrive in the Commonwealth, at which point you're really out to find the Institute and choose a faction to work with and deal with the other factions.

Skipping Other Quests by Going Directly to Areas

The Memory Den
You can go directly to Goodneighbor and the Memory Den, use it to re-experience the abduction and be directed to Nick Valentine that way, as opposed to going to his office, freeing him, then the Memory Den.

Nick Valentine is Required
You can also go straight to Vault 114 and rescue Nick Valentine and auto-finish the quest 'Jewel of the Commonwealth'. From there, things proceed the same. It doesn't matter if you have Dogmeat or not, as Nick can call him himself and you'll still be led to Kellogg's house.

Reunions
So you can quickly get to the 'Reunions' Quest (which requires 'Getting a Clue' and investigating Kellogg's house), simply by going to rescue Nick Valentine from Vault 114 as soon as you feel strong enough to face the trigger men.

A trip to the Memory Den with Kellogg's brain augmentation will be required to locate the Institute afterward, but it's entirely up to you as far as the early game!

Why this is Good
Some players like myself don't want to do things the exact same way the second time through (I myself plan a new character when Automatron releases), and this offers a lot of flexibility in your adventuring. You'll be led to Fort Hagen, the BoS will arrive, you can locate the Institute with the Memory Den after Kellogg is finished, and you'll be good to go from there in finding them.

Options open up even more once you've met the Institute, and every faction in Fallout 4 can lead you to the end-game in their own way (though they'll always want you to finish off two others).