MTV Geek has the entire interview: http://m.mtv.com/geek/article.rbml?id=2012/10/26/jon-m-chu-lxd-gi-joe-2-masters-of-the-universe/&weburl=http%3A%2F%2Fgeek-news.mtv.com%2F2012%2F10%2F26%2Fjon-m-chu-lxd-gi-joe-2-masters-of-the-universe%2F&alt=http%3A%2F%2Fm.mtv.com%2Fgeek%2Fblog.rbml&cid=300

But here is the relevant part related to GI Joe:

Getting back to G.I. Joe: Retaliation, Chu noted that the sequel hit a significant hitch earlier this year, when the studio delayed the impending Summer release in order to post-convert the movie to 3-D. “I really want to push how we use the 3-D,” said Chu. “Especially since we pushed the movie date, I want to fulfill the promise to the fans that the 3-D will be great, and enhances the experience of the movie. So every step of the way, I’m in that room, watching… It’s hurting my eyes, but we’re getting it better, and pushing it further.”
Continuing, Chu added that most post-conversions simply sink the background, and allow that to stand in for the 3-D experience. Not so for the director of Step Up 3D. “I shot two 3-D movies,” said Chu. “So being around that, I know what we are actually capable of doing. If we had shot it in 3-D, there’s a lot of things that we would shot in a 3D way.
“Fortunately, a lot of our shots, I guess it was in my brain anyway,” continued Chu, laughing. “We had a lot of depth in our shots, or let our shots play longer. For me, if we’re going to do this, we have to make sure it enhances the experience. That’s where we are right now, and it’s a slow painful process, to be honest!”
Even though the movie is technically done, and with no natively shot 3-D footage, all the shots need to be post-converted, that doesn’t mean Chu has given up on making some tweaks. “I’m trying to convince them to give me a couple days to do a couple of enhancements,” said Chu. “But as of right now, we’ll see what they let me do. I really want to shoot some of the sections in 3-D to give it that edge… But we’ll see if time permits, and they’re down to do that.”