It's those realizations that are leading me to adjust my expectations. The idea of "setting up runs" in the open environment is in direct opposition to having an immersive, epic, mysterious sci-fi title IMO. Once you start thinking of the play area in terms like that, I don't think the game can deliver on its narrative aspirations. At that point it becomes a loot factory and a mechanics playground which is pretty much what the Alpha + Beta have felt like. That's fine, as I said I've been having a lot of fun, but going back to the original point, I don't think the story can be the draw of Destiny in that case.
I don't see how this will effect the story at all. I don't think a game needs to go out of its way to ensure the gameplay falls directly in line with the story, or to strive to be realistic to provide immersion.
If they wrote the best sci-fi story we've ever seen and linked it via cutscenes with specific enemy enounters tying in to focal points of the narrative, that's all they'd really need to do to provide a link, it wouldn't cheapen the effect just because the enemies respawn like an mmo.
I don't think it matter much anyway, I think Destiny's story is going to be in the background.