Poor acting, wack dialog, lack of internal logic with some scenes.
First episode wasn't horrible, but it was FAR from flawless and as many have said it never had anything to make viewed feel they NEED to see the next episode.
It's not about huge action sequences or expecting known marvel characters. A good example of how a show like this could have a GREAT first episode is Fringe. The shows have similar concepts and probably had similar budgets.
The acting on Fringe was FAR superior and they weren't trying too hard to be funny with the dialog, they also had things to hook the viewer into to seeing the following episode.
The acting in SHIELD was hit or miss. Coulson, May, Peterson, and the Doctor were all well acted but the other actors weren't very good at all. The dialog was trying too hard to be funny (especially with the Sky character) but fell flat because the actors weren't strong enough. There was also no real hook to the show (beyond some people knowing Whedon shows get better as they go along).