Probably the BOS, but is has the unfair advantage of being a recurring faction, meaning it has had more than just Fallout 4 to develop, unlike the other factions.

As for a secondary faction....probably Children of Atom, again because they got development in a prior in a game.

Eh, Children of Atom were only a minor faction in 3. 4 is where they were more fleshed out, and in Far Harbor they really shined. And not just with the green glow of excessive radiation.

Yeah you are right, but I couldn't for life of me think of a properly developed, secondary faction. Gunners are generic bad guys, triggermen are generic bad guys, rust devils look cool but are still generic bad guys.

I think maybe the BoS, it showed different characters witb different goals and personalities and while some were devoted more than others, you could still choose who to love and who to hate. The other factions don’t have much NPC dialogue/terminal entries that could describe the members’ motivation. We know almost nothing about Railroad and Minutemen members (except Preston’s small squad and Deacon) and Institute personnel mostly talk/write about work.

For a secondary faction, I liked Far Harbor. I just wish they had more “prove yourself” quests, because catching mirelurks was kinda fun with the celebration afterwards. Nothing like the other factions that love you on the first sight.

As for the main game, none of the secondary factions were developed enough.

Yeah, felt like the Brotherhood's campaign had the most put into it, but that's no surprise for the series' darling faction, even if this incarnation was less than... suited to everyone's tastes.

The Atom cats were my favorite side faction, and do pretty well against the base game competition, but by the time all the DLCs were out, the Church of Atom had significantly more content.

Special shout out to the Commonwealth named raiders, though. The terminal entries and things which changed dynamically as you killed certain groups led by named raiders, as the fear and gossip makes it to other groups? A fantastic detail, even if not enough to shoot them into the top.

The Minutemen had a lot of potential, and it's cool they were based on a historical group unique to the region, but their implementation is weak and their quests boring and repetitive. The Brotherhood is probably the best developed out of the big four.

Too many of the side factions were too generic, the Children of Atom are the most fleshed out and at least somewhat unique.

With DLCs Included, Children of Atom, and the Nuka World Raider Groups.

BOS I feel like was the most developed/consistent, but as said they had the advantage of being a recurring major faction.

In terms of who received the most development in F4 specifically, the other three major factions were either entirely new (Minutemen), or extrapolated from a single mission in F3 (The Institute and the Railroad).

Personally I feel that the Institute received the most time and development, being so core to the main story and arguably the antagonist faction, but in a lot of ways they came across on the undercooked side.

Hmmm when it comes to my opinion on which factions had more effort in them... hmm I'm gonna look at them from a lore stand point but only the factions exclusive to 4. So BoS not included.

I feel like the Children of Atom has the most effort lore wise and that after that would be The Institute

Then Railroad

Nuka World Raiders

Commonwealth Raiders and Minutemen tie.

Honestly I really like the CoA

Probably the BoS. But like it’s already been stated they have had so much time to develop. Other than them, I would really like to say the Minutemen, I like hearing about them dying out and stuff.

For a minor faction, I think the Children of Atom. But I agree with @Dyre Wolf Cub , I really liked the depth that went into the Raiders around the Commonwealth. Really wish you could have done more with them as a bad character but oh well.