As for the Strand plotlines:
If you want a really difficult story which is quite entertaining, and to end up with a very useful weapon, go for the Igzadra. Be warned: many missions involve long searches and muchos carnage. In terms of the final battle, its difficult, but nowhere near as ridiculous as the Ziddy one.
If you want an easier string with possibly a less exciting storyline, but one which uses the game engine in interesting ways, go for the Agdzari or whatever. Some of their missions are interesting, and one of them could give you access to an indestructable ship (if you're a mission-aborting-backstabbing git, that is). Final battle is laughably simple.
My advice? Go for all three with the wonderful Triple Agent plugin. And be thankful you don't have to use said plug's first incarnation like us old fogies. "Okay, zip across this huge twelve-jump stretch in 12 days! Okay, now fight 47 Crescent Warships! Done? Do it again! Okay, now zip back to where you started! Did we mention there's only a 0.0001% chance of getting these missions?"