Ive been wondering what Blackreach really has to do with the story in Skyrim besides being a subzone for the main quest. For some reason I have a feeling it has something bigger in there. (If not, there should be)

I'm pretty sure it's a major Falmer city, basically.

Meh, Falmer dont really do all that much for the lore part of it, and I mean, GIANT MUSHROOMS, DWEMER RUINS, GIANT SPHERE OF LIGHT-STUFF, GIGANTIC BLUE MULTI-MUSHROOM, OTHER DWEMER RUINS. I mean, doesnt that large ball in the Dwemer fortress or something count? What about that giant multi-blue colored muchroom. I feel there should be more behind it. DLC maybe.

Well there is a pretty awesome easter egg in there involving a certain famous alchemist.

It's not an easter egg, it's an actual quest.

As for the city: it was a major Dwemer city that existed outside of Nord sight so well that nobody knew it existed for a long time. The Falmer were driven from the surface by the Nords and sought refuge with the Dwemer, who blinded and enslaved them. Then the Dwemer disappeared.

just because its a quest doesn't make it not a easter egg.