First off, Chloe continues to be completely worthless. I sense this will be a running theme. Also, Eli needs to grow a pair.
I think you're missing a major point of this new series. It has been repeatedly said, both by characters on the show and in promo material, that the characters aboard the Destiny are the "wrong people". Some of them are soldiers and scientists who were going to go through the gate to explore the Ninth Chevron anyway . . . but many of them were never supposed to step through that gate. Eli and Chloe are only two of the folks who shouldn't be there and are the "wrong people".
It's actually a major aspect of Chloe's character that she is "useless". She isn't a scientist or military person, she has no "job" to do on the ship, and she doesn't know what to do with herself. She feels in the way. And to top it all off, of course, her father died just a few days ago (in story) and she feels very alone and purposeless. In fact, as she was her father's assistant, he WAS her purpose and now he's gone. I expect we'll be exploring this quite a bit more as the series progresses.
And please, Eli needs to "grow a pair"? And so do a good portion of the audience watching this show! Eli is a geek with serious self-esteem issues. He's freaking brilliant, but so what? He's a college dropout who very well may never have seen a woman naked before!!! Sadly, while not as bad off as that, I identify pretty strongly with Eli's character. I'm not that brilliant and I've had somewhat better luck with the ladies . . . . but it isn't an easy thing at all for somebody with self-esteem issues to simply "grow a pair" and try to start a relationship.
Besides, Eli mooning over Chloe while she gets involved with Scott gives us some dramatic tension. I like Scott's character and it makes me happy to see him connecting with Chloe, but at the same time I identify with Eli and I feel bad that he's mooning over Chloe and feels, perhaps rightly, that he has no chance with her. He is becoming friends with Scott, but is also very jealous of him as well.
In my opinion, that makes for some good TV!!!
This is not a show where four heroes step through the stargate every week and kick some ass!