Is there a "none of the above" option?
In the comics it was clear both sides lost sight of things and were royally screwing up. Stark used disaster (and created some, but that's another story) to push for every pet project her ever had in mind about making the Avengers more pro-active and global. The extent to which he went "with us or against us" should put anyone into worry mode. On the other hand, Cap ignored legitimate if somewhat irrationally caused (new york can become a war zone every few weeks and no one blinks, blow up one school...) fear the public had and basically decided to beat up Iron Man's side until the public stopped being stupid.
In the movie, based on what we know, unless the Inhumans on SHIELD get a namedrop, which would make me lean more Iron Man for reasons others have mentioned about super-powers popping up in the untrained and potentially criminal, based on the movies, exactly how much point is there in registering "superpowers"? Alien invasions are beyond any hero's control, and most of the other fights were scientists playing with toys hard to control until after the fact. That leaves the Hulk's rampages, and you're really only holding him in check if he lets you. What can they do, register anyone smart enough to build a super-suit of armor and watch them 24/7?
On the other hand, what exactly is going to be different beyond what SHIELD's MO was in season 1? Find, track, and deal with renegade super powered people. Unless Stark, Ross, or someone else starts going crazy with plans, it seems just an effort to get back to status quo, which seems stupid to fight against. I suppose there's a logical argument for hydra infiltration, but that's an argument for proper vetting.
It seems like this could be another pointless fight between people missing the point of why they're fighting, whcih granted, was the end message of the comics, even if they had to let one side "win".