Well after Ghost Widow, I would say Scirroco has the best story. Mako and Black Scorpion are just to blatant about their motives to provide an engaging story.
It's not how many times you get knocked down that count. It's how many times you get up.
I agree that Scirroco's story is pretty good. He is almost likeable (from the point of view of someone who almost always plays blue side).
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Scirocco's arc, by far, is my favorite. Lots of unique maps, too.
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I have to admit that I'm fond of Black Scorpion's arc as it reminds me of one of my favorite Iron Man arcs. Mako's was okay. Scirocco's is indeed good.
I clicked Black Scorpion instead of Mako the other night, was a little irked. I hadn't done Mako's past the patron pools before and wanted to give it a shot. Finished BS's patron pool part in about 20 minutes. (Claws/Elec brute)
I really like 'Rocco's arc, but if you have a dislike of Mu you may want to try a different one.
If you're truly playing for story, I'll ditto Scirocco. Fair warning - not just because of Mu, but his arc is the most challenging, with more Hero/AVs than the other arcs. Yes they can be downgraded but they're still tough. Make sure you play the 2nd arc as well and not just quit when you get your patron powers after the first arc, the 2nd is when the story gets good.
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For the longest time, it was the only time in-game when you could face off with WISDOM. Still no Spark Blade or Rose Star, but even so--Mirror Spirit's mirror teleport is cruelly awesome.
And because it's worth noting more than once: awesome maps.
There are no words for what this community, and the friends I have made here mean to me. Please know that I care for all of you, yes, even you. If you Twitter, I'm MrThan. If you're Unleashed, I'm dumps. I'll try and get registered on the Titan Forums as well. Peace, and thanks for the best nine years anyone could ever ask for.
Hmmmm... Scirocco sounds good. I think I'll have to give that a spin. As for facing a lot of heroes, well if I can solo the Maria Jenkins arc, I figure I might manage it. Pack a lot of lucks and a metric ton of recharge. 
Thanks folks
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I like Iron Scorpion's for the opportunity to fight Scorpinoids and Arachnoids. Also, isn't his the one with the big nemesis invasion of grandville on the beaches where all the Arachnos heavies are present as NPCs holding a line while you go out and take down mole machines and fake nem leaders?
I love that mission but always forget which arc.
Scirocco's is the best except I loathe Mu. It's really funny to see the good Ice Mistral.
Mako's one virtue is that except for two defeat all's it's easy to speed through. Well, ok two virtues: getting to beat down Ace McKnight a second time is fun also =)
Ghost Widow's is ok, but really I like the earlier arc for her with Seer Mano or whatver her name is back in Mercy Island where you help Wretch and Ghost Widow against some traitors.
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Having done them all now , Scir's is the best one I think, story-wise. There are EBs and Mu everywhere, as has already been mentioned, and if you end up being fond of the guy at all (Like my Stalker did- 
) it can be a little sad, but it's still a good run.
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Hi folks.
Having just dinged my latest 50 tonight, my Fire/Fire Blaster is on his way redside to pick up Scorpion Shield just as soon as I've spent all my Hero Merits.
Which patron arc would you recommend out of the four? I like to play for story so I'm wondering which were the most appealing to you. I have run Ghost Widow's twice I believe so I'm not in a hurry to repeat that. Recommendations welcomed! Thanks.
@Dante EU - Union Roleplayer and Altisis Victim
The Militia: Union RP Supergroup - www.themilitia.org.uk