For me, my favorite eras, in order:
Levitz/Giffen (up to, but NOT including The Magic Wars)-To me, this is the pinnacle of the Legion. And my understanding is that we’re getting these guys back up to Legion 16-ish (just before the Crisis stuff. So just pre-Sensor-Girl.)
Shooter, take 1 (Adventure 346-380, but not, REPEAT NOT the dreadful Action backups). My two all-time favorite Legion stories are here: the first Mordru story and the second Universo story (the two-part one))
The post-Zero Hour Legion thru the Cho Sting storyline
The Legion Lost stuff–if you read it in a big batch, it’s wonderful. I loathed it when it was coming out. It was a refreshing change from watching Roger Stern regurgitate old stories. And I like that they had the guts to look at the damage that had been done to the characters (Element Lad in particular) and deal with it rather than just ignore it.
The Levitz stuff (the Earthwar stuff)–it’s uneven but wonderful stuff and you have to credit him for the attempt to attempt to do a Marvel style multi-part saga.
The Cockrum/Grell stuff.–It was fun watching them try to grow into a more mature, Marvel-esque book.
The pre-Shooter Legions. (TONS of energy–and unabashed silliness (the “Interplanetary Chance Machine”, anyone?) but with actual drama too (Lightning Lad losing an arm, dying, etc))
The Waid “Eat it, Grandpa” Legion. An attempt to do something truly different with the Legion. Plus I loved the costume designs (Sun-Boy in particular).
Runs I didn’t like (not in any order):
The godawful Gerry Conway run (when SatLoSH became LoSH) pre-Levitz/Giffen. But, really, any team book Conway ever wrote sucked. Remember “Vibe”? How 'bout “Invisible Girl has an affair with Subby and starts divorce procedings because Reed stops Franklin from destroying the universe”.
The “5 Years Later” stuff: I admire Giffen’s attempt, but because of constant editorial interference (two editor mandated reboots in two issues?!), plus the fact that Giffen has admitted that he was just winging it–no uber-plan in mind–it meanders too much. A good try, but ultimately a failed one, IMO.
The Stern one (from post-Cho sting through Legion Lost)–too much was typical '90s “Hi! We know you miss these old characters, so we’re going to cock-tease you with them.”, reguritated plotlines, and his characterization of Phantom Girl, Ultra Boy, Element Lad and others was atrocious.
The Tom/Mary Bierbaum stuff–was there ANY fanwank theory they didn’t embrace? Lightning Lad was really Proty but Saturn Girl was too dumb to notice? Element Lad HAS to be gay 'cause he wears pink? Etc. I hated every change they made (although the annual with Glorith and Ultra Boy rocked).