G.I. Joe: Retaliation was testing poorly and needed reshoots, according to Deadline, which is why the release date was pushed back from June to 2013 (see "Universal Moves 'G.I. Joe: Retaliation' to March 2013").  Channing Tatum, who’s gotten hot since the first film, was going to be killed off early in the sequel, but was one of the few things testing audiences liked. Reshoots will help expand his role and keep him alive.  And the 3D move was essential, given how the dollars on the summer blockbusters have flowed.
The delay of the movie at this late stage, when theaters were booked and licensed merchandise had started to flow (see "'G.I. Joe' Toys Interrupted"), was a radical move, reflecting the degree of risk Paramount perceived in releasing the movie as it was and the size of the opportunity in fixing it.