Well, this got me curious since I haven't really been keeping track of faction or MQ quest lines since I've been building. Was really shocked on what I found. Based on the game manual, you appear to be correct.....
Fallout 4 only has a total of 4 factions:
Number of MQ quests :
!!?!

<-- Note: Skyrim: 19 Fallout NV: 100 (with 81 unmarked miscellaneous side quests)
Number of Institute quests (to include side/favor faction quests & radiant quests):
Number of BoS quests (to include side/favor faction quests & radiant quests):
Number of Railroad quests (to include side/favor faction quests & radiant quests):
Number of Minute Men quests (to include side/favor faction quests & radiant quests):
Number of miscellaneous side quests not related to a faction:
The base game for NV had a minimum of 13 factions (which was really 16 factions when you factored in the 4 different raider tribes). And all of these except the raider tribes had several faction/favor related quests.
Also for comparison, Skyrim had a minimum of 13 factions (not including the extra factions that came with DG or DB DLC). Skyrim's faction quests averaged some 16-20 quests per faction. And that doesn't include the miscellaneous sandbox side quests like the Great Tresaure Hunt, Collection mini game, becoming nobility i.e. Thane of all the holds, or building your own home/getting married etc.
So I would propose 2 likely reasons why this may likely be so:
1. Voice acting for not just 1 but 2 protagonists. And completely unnecessary scripting to allow free camera shot close ups for views of the protagonist facial expressions while they're speaking to just about every vendor in the wasteland. That took up a significant amount of development resources and time. Which could've gone into increasing the MQ and number of side quests, content (such as a greater variety of weapon types etc). Or better yet, into QA to review the horrific, and non-intuitive UI and speech interface which was clearly designed for the console platform.
2. The settlement feature. I personally LOVE this feature and it's clear Beth dedicated a lot of development reources/man hours in making this stable and reasonably bug free. I've yet to run into any bugs or glitches in any building scenarios in my settlements. However, those [censored] who don't care for this amazing sandbox aspect, will complain that this detracted from the other questing/weapon content in previous games.
The voice bsa archive file for FO4 is 2.5 GB alone--this doesn't include the sounds bsa files which hold the radio station sound file data. The corresponding voice file size in NV was 1.6GB. So I personally find the Diamond City radio selection VERY limited at some 38 songs (a mere 45.6 MB compared to the 48 mp3's that the vanilla version of Radio NV had at some 269MB total. So the trade off for the new voice acting for traditional features like more radio stations was a let down for me. Particularly since listening to Diamond City becomes really hard on the ear by the 3rd recycle of the playlist. And the station's maniac depressive DJ makes listening to that station even worse. 
*note to self, murder the Diamond City DJ at the earliest opportunity*
So yeah, I do agree with you OP. Particularly since the existence of #1 implies loads of more game content and quests could've been added in lieu of the PC voice acting files. Also the radio station selection is a bit lacking. But then again, I've been horribly spoiled by NV mods like CONELRAD, Hepcat radio, Wave Radio etc. But it will be a while yet before I complete the MQ and faction quest lines in the game. And I'm replaying with a different faction alignment as a female PC next time around. The degree of replay (minus the sandbox random settlement feature attacks) appears to be somewhat limited. So I'll likely return to playing Skyrim full time until the modders get their hands on the game next year. 