My persojnal favorite is the ebonheart pact story.
Why?
...because its the only one that gives me a decent background for the three banners war going on, that actually makes me want to go to Cyrodil! (and generally, I dislike that sort of thing, not in the least because I kinda suck at PvPness...)

I mean, let's review...

Aldmeri Dominion - first we have to deal with sea elf invasion attempts, then court intrigue, hidden racist traitors and near civil war, then go on to political movings to tie the fragile dominion together while putting out bush fires left and right, and end up stumbling over even more of the same old court intrigue, which once resolved, doesn't stay dead (literally), creating more problems, until finally... we get a new chapter where a spurned lover is willing to burn down the world to force his lost love back under his thrall, and once that's done, and you are thouroughly sick of forests at that point unless you end up channeling "Poison Ivy" (though that's an entirely different universe), a imperial incursion spawned malign ghost messing with the kitties.
Razum-dar makes the whole thing more bearable, though that is easily balanced by all the racist altmer strutting their silly notions as if they were the aedras gift to nirn (quite literally, considering that is pretty much the core of their belief) but at the end of it I keep wondering how the dominion ever deserves to survive, with so many of them working at cross-purposes... and why the fu... uhm... I mean, why in the divines names they think -they- are the ones who should make the decisions for all of tamriel when they can barely keep themselves from civil war, and why my poor characters ought to go to cyrodil fight for That???

Daggerfall Covenant - here we get to deal with division in the ranks, right from the start... redguards and bretons in trouble with each other, unused to the new alliance yet, and orcs still holding grudges against bretons even while beset by cultists (a theme! Bretons are kinda scummy when you look past the facade and at their history, huh?), then go get to save said bretons from the aforementioned reachmage cult and undead werewolves, to go on to save more bretons from cultists exploiting the aforementioned grudges and rifts between the cultures, then go on to deal with a personal grudge turned all out civil war thanks to an ancient vampirification artifact, which you end up turning over to friggin Molag Bal in the final approach (which kinda goes completely against all the mainstory feels IMO), only to go on to help the redguards dealing with necromancers while wanting to slap pretty much every single one of them along the way for their foolish "Oh, I cannot fight my ancestors even tho they are undead wanting to eat my childrens branes right now..." and then move on to a double feature, dealing with both reachmen again and also impariel invaders, all the while getting more and more disgusted with the covenant leaders stupidity... up to the point where you have to actually resurrect their high king from the results of his own "Let's charge on unprepared! It'll work out somehow..." idiocy... and just like with the dominion, you are left wondering how any of them should ever be handed the fate of tamriel, and why you ought to fight in cyrodil to plant their royal ars... uhm... behind on the ruby throne.

Ebonheart Pact - that one starts right with a body blow, the DC invasion of bleakrock and bal foyen, a desperate flight and defense, with the "starter" choice being hefty and painfull compared to the other two (I mean... has anyone checked the fort/docks after saving the other? What's the "to nercomance or not to necromance" of the DC or the "to revenge or not revenge" of the AD compared to all those dead NPCs?) Then we follow that plot, and deal with more invasion troubles, and face how far the dunmer are prepared to go when desperate, and the fallout from it, all the while see the damage done by covenant forces along the way, be it despoiled magic schools, ransacked farms, or their corpse soldiers, and when we finally dealt with the fallout from all that, we get a breather moving on... kidding! We get to fight cultists using biological weapons pursuing revolution fuelled by the cult leaders personal revenge schemes, then go on to face the next incursion - this time, forces from the dominion using deadric magic in an attempt to genocide the friendly neighborhood lizardmen, before moving on to deal with covenant-supported civil war in the lands of ice and snow, and once that's done, move for a "find the artifact" scrap-hunt through cultists and barbarians, with a worm cult powered ghost-giant thrown in for good measure...
All in itself, nothing to beat out the other alliances quest-ploys, but... you get a idea why the pact forces fight in cyrodil, and its not for lackluster Jorunn to claim the ruby throne, its to keep their lands free from the other jer... uhm... rulers. Well, and for revenge. Makes me wish we pact PvPlayers could get an pact-isized warcry... "Remember Bleakrock! For Bal Foyen!! Never Again!!!"

Which is totally in sync with the pact history of course... the three races -only- came together to defend each other after all!
https://www.youtube.com/watch?v=2-lGevvO2vw
Blood For The Pact!