So you start your post out saying most quests are enjoyable then spend the rest of your post explaining why the quests in this game are bad & boring (enough to even make you not bother completing them)
Maybe I didn't make it clear enough
First time you play through the story they are very enjoyable (Except the last mission), the second time, you have to watch all the cutscenes and do the same BDs, which is to be expected. However even all the enemies are more or less the same places as well, so even they can't surprise you. At least in gigs, you might approach it from a different direction, the patrols might be another place etc. And usually the areas are more open so you can do them whatever way you want. Whereas many of the main stories, doesn't allow this and you just have to follow this linear path through them.
I didn't bother with the cyberguys, because there were to many of them and they were pretty much all the same from what I could see. The reason I stopped with the gigs, was because I could 1 shot pretty much everything and therefore it was no longer funny to do them then, and I didn't need the money anyway, which is what you get from doing them.
Therefore I went on to complete the game and that last mission was as easy as a standard gig, but also repetitive with how the enemies spawns, each floor etc. To then finally having to fight Adam Smasher, which I didn't care about at all, I think my character had seen him two times in my 125 hour play through and both of these where in the heist, where its basically a cutscene, he weren't a threat to me or interfered with anything I did, so I didn't care. I didn't even get the impression that Silverhand cared, he said that it was because of Rogue, but even she say that it have nothing to do with Adam Smasher.
So to me, the final boss, was a character that none of the ingame characters really cared about and I as player didn't care for either, I saw him in the beginning and then again 123-124 hours later, where he is then the big bad boss?
So I enjoyed the whole story the first time playing through it, except the last mission. But looking back and having played a bit on another character, these story mission, just weren't funny, because in the first play through you thought these missions occured because of what you had chosen in dialogs. But when that illusion is broken and you end up doing them regardless of what life path or dialog option you chose, and the enemies are standing the exact same places etc. they become boring to me.
Hope that made it a bit more clear.