-The dark brotherhood forever: I believe you get radiant, generic no name NPCs to assassinate. I didn't go very far and been some time since I played DB, but I don't think you ever wind up assassinating a named NPC
-No stone Unturned: It can be fun in all the interesting places you wind up exploring, but yeah, once you have the reward is a pittance compared to the tediousness of the whole thing.
-Impatience of a saint: Again, agreed - tedious. Can be a good enchanted necklace reward if you don't have a better one already and thankfully it is relegated to the Soul Cairn instead of all of Skyrim. All-be-it the Soul Cairn itself can be a tedious place.
and for the misc:
-find resonance gems to complete Kagrumez trials: I think this one can be worth it. You find two in Kagrumez. One is for sale by the Land Strider caretaker. You find the fourth one in another Dwemer ruin somewhere on Solstheim.
-Bring ancient falmer tome to Urag. I think there are only four books. Gives some decent gold, but that's it AFAIR.
-Locate east empire pendants: Yeah mainly good for gold early on in the game. I'm not sure if there is any extra reward for finding them all.
You can always do radiant quests (Jarl, Innkeepers, the guilds). There should be plenty of side quest that NPCs give in each town. Some don't get unlocked until you reach certain points in the main quests. There is also the dragon priest mask collection. You may find that tedious compared to the final reward but some of the masks themselves are quite nice. Plus you get safe storage in Labyrinthian even before you start looking for any of the masks, I believe.
Then this mod at the very least is a must. http://www.nexusmods.com/skyrimspecialedition/mods/266/? This patch fixes up a tonne of bugs left behind by Bethesda and done quite well too. Only a handful might be subjective fixes, but otherwise the patch fixes quite a bit.