Omo makes a remark in RIUVA's comments:

2. Reading various bloggers’ reactions and comments on ef tells me one thing (and many others, but): people tend to either “get” the Chihiro story or the Miyako story. Very few people get both and how they really relate to each other. Fewer still get how they relate to each other before seeing the last episode. You are pretty much just in the Chihiro camp. I think this is the biggest failure of ef anime (especially given its role in the franchise), so it’s not really a fault of the people who don’t get it…. but to me it seems as plain as day.

He does not bother to explain in plain words to us plebes how the stories were connected or intended to be connected. Fortunately Kuro gives it a shot at #animeblogger:

<kur0gan3> not material enough? <zaitcev> "Very few people get both and how they really relate to each other." <kur0gan3> he already said that the stories explore the opposing sides of the same theme. <zaitcev> However, the main point of my critique was that the stories were insufficiently connected, and Omo is taking aim very squarely at it. [Omo does allow, however, that not having "it" explicit was "the biggest failure" — Author] <kur0gan3> oh <kur0gan3> insufficiently connected? <kur0gan3> well <kur0gan3> maybe not physically, but thematically, they are. ... <kur0gan3> Hiro's main theme is mainly "dreams" <kur0gan3> he dreams of being a real manga-ka, but he's held back by his relationship with Kei <kur0gan3> more like, Kei's nagging. <zaitcev> ok. <kur0gan3> what finally frees him is when he realizes his feelings for Miyako <zaitcev> I think I never saw Chihiro dreaming. Maybe she cannot, because I heard REM sleep is what actually re-packs memories into long-term areas. ... <zaitcev> So, ok. Dreams are the theme. How do they oppose Chihiro? And her theme is the direct memory and recall, probably. <kur0gan3> well <kur0gan3> i can put it in this way <kur0gan3> both stories have "dreams" and "memories" as their themes, in Chihiro's story, "memories" are the main, "dreams" are the supporting, vice versa in Miyako's story.

Sounds pretty convincing. But then Omo himsef drops this hint:

Like how the two storylines explore opposite sides of the same theme, for example. // It’s no coincidence that Renji was doing a career survey.

Yes, we orz in front of your cranium, are you happy now? Happy enough to explain your reasoning?