Well its 2 groups going for the same goal. What did you expect? If group A and group B need something from location 1, then why would group A or group B go anywhere else?
"More content? Nah it's ok Bethesda. I can settle for copy-pasted work, thanks!!

"
Seriously why would you NOT want different questlines? The guilds have the same questlines BECAUSE Bethesda designed them that way. To say it makes sense for the story is kind of a moot point, as Bethesda can take the story in any direction they want, but chose an easy route where both decisions intertwined and resulted in a very similar product.