I read it (or most of it) when it first came out. I was about ten or eleven and very much a Marvel guy - Legion, Teen Titans and, a year or two later, Firestorm were the only DC comics properties I rated as highly as Marvel's comics. I'd read about four Legion comics before The Great Darkness Saga, and I really liked the concept of the comic, but TGDS was on a whole new level.
I'm just going to be repeating what a lot of people have said already, but part of the joy in reading the Legion was the fact that they so obviously had a rich and complex history that a new reader would just get the odd reference to, and you'd have to piece it all together. I think someone here said it was immersive, and that's exactly right - it was Star Trek for super-heroes. With TGDS we suddenly had an epic story, one with a villain or villains who could actually convincingly challenge powerhouses like Mon-El, Ultra-Boy, Superboy, Wildfire... the whole team was struggling to even win one battle, and there was the big mystery of who the bad guy was (I didn't even know Darkseid, and it was still great).
As others have said, Giffen's art was unique and ground-breaking - for one thing, it was the first comic where I'd seen colour drawings without a black-line to define them. That was a pretty cool special-effect back in the day of limited colours and low-quality paper. The story blew me away then, and I still think it is one of the best stories I've read in comics, though admittedly nostalgia plays a part. It's certainly in my top ten DC comic stories, one of the greats of my youth.