I liked both MQ.
But FONV had a lot deeper narrative just because there was so much more.
The MQ in F3 only had two sides, good and evil, while the MQ in FONV had 3 sides.
And if you look at the side quests, there was 17 in F3 compared to over 4 times that many in FONV.
Bethesda obviously took this to heart in Skyrim which had a lot more quest lines.
Quantity has a quality all its own.
The two MQ were not bad, but is was obvious that they ran out of time for some of the elements in the Civil war MQ.
Still there were the two Main Quests, plus the huge faction quests some of which were very good, plus a host of others quests.
With a map just as big as Skyrim, Bethesda not developing a totally new game engine, and the extra time they took, I really can't see Fallout 4 not having more real quests than Skyrim.
If nothing else there are 12 companions and each of them should have multiple quests plus the Synths/Railroad, the Institute, the Brotherhood, and a host of mutants, zombies, and raiders.
With the extra time and attention paid to the Narrative, I expect the main quests to be better than Skyrim's.
Anything better than that is a bonus.
And with 400 hours of play, it is obvious that Bethesda decided to go for both quality and quantity.
Maybe they can delivery on the former, but I know they will delivery on the latter.