From all that we've seen of G.I. Joe: Retaliation it looks like an action packed summer flick with ninjas fighting on cliff walls and The Rock blowing stuff up. It's hard to imagine that they could mess something like that up, but evidently the film did not test well with audiences at all and that is the biggest reason behind the recent delay. Previously the studio had claimed that it was for a 3D conversion, but signs point to the bigger reason being poor testing.
This also gives the filmmakers a chance to put more Channing Tatum into the film. He's become a pretty big deal after headlining two hits in the past year (The Vow and 21 Jump Street) and now they want to show him off... instead of killing him off. That's right. Tatum dies in the film, or he did. Sorry, about the spoiler, but it really isn't a spoiler anymore. Now with him being a big star and test audiences complaining that he and The Rock didn't bond enough in the film for their liking the studio is going back to film again.
I think any other summer this movie would be getting released on time, but with Battleship bombing and the entire industry nervous thanks to the failure of John Carter Paramount is clearly playing it safe, even if that costs them a lot of money.
A full explanation for the delay from one of Deadline's sources is below. He fails to mention that G.I. Joe would also be competing with Tatum's abs since Magic Mike comes out the same weekend Joe was originally scheduled to.