Pacific Rim is a massive undertaking in terms of special effects requirements, as well as the sci-fi concepts present in Travis Beacham's original script draft - such as robotic machinery operated by a "neurological bridge" between humans - not to mention, the plot involves sky-scraping robots battling similarly-massive creatures from another dimension.
However, at Comic-Con, director Guillermo del Toro revealed that he resisted utilizing certain modern-effects tools (ex. motion-capture) that similar large-scale productions (Avatar, The Avengers) have relied upon - as it would not have fit his approach. It's for similar reasons the filmmaker refrained from shooting Pacific Rim in 3D, while expressing little to no interest in converting the project to 3D during post-production.
Warner Bros., on the other hand, isn't so hesitant about post-converting films to 3D. Filmmaking is, after all, a business first, a form of artistic expression second - from the investor's perspective, that is - and the studio has significantly boosted its financial returns on big-budget fare with post-3D in the past (see: the Harry Potter and Clash of the Titans franchises). Hence, it's not surprising to learn that Warner Bros. has "strong-armed" del Toro in post-converting Pacific Rim to 3D, as Variety puts it.
Here is del Toro's previous explanation for why he did not shoot Pacific Rim in 3D:
“Originally there was a discussion that took a long time to overcome that was to make the movie 3D. And I didn’t want to make the movie 3D because when you have things that big… the thing that happens naturally, you’re looking at two buildings lets say at 300 feet [away], if you move there is no parallax. They’re so big that, in 3D, you barely notice anything no matter how fast you move. To force the 3D effects for robots and monsters that are supposed to be big you are making their [perspective] miniaturized, making them human scale.”
Michael Bay demonstrated with Transformers: Dark of the Moon that a film featuring enormous digitally-rendered robots can, in fact, look quite spectacular in 3D - IF the action scenes and CGI-heavy set pieces are carefully composed and constructed with 3D in mind, of course. With Pacific Rim, however, del Toro has made it no secret that he's gone out of his way to make the film feel more visceral and realistic - even splashing oil on the camera lens at times, so that the action has a more visceral and immediate feel.
In short: del Toro's indicated that Pacific Rim simply isn't a movie meant for 3D. That sets it apart from recent 2D films that were designed with 3D in mind - and thus, actually benefited from the "upgrade" (ex. The Avengers). While it's possible that del Toro's love letter to giant monster movies could ultimately follow suit, it might be best to remain skeptical for the time being.
Of course, 2D viewing will still be an option when Pacific Rim opens in theaters on July 12th, 2013.