Sandbox is great, but much like cover based shooting systems it has flaws.
Cover based systems seem to be a bit broken; some games such as Uncharted and Rainbox Six seem to get it right: If you've got a single body part poking out it will be shot. On the other hand neither of those games have piercing and that kinda bugs me. I'm hiding behind a thin (supposed) brick wall and the sniper who spotted me can't get his rounds through the wall. Also some games leave body parts obviously exposed (sorry Alpha Protocol, you'll have to take this bullet) but the bad guys just want to aim at the wall instead of my exposed hand/foot/knee/scalp.
Sandboxes are great, but get really distracting. To this day I've not completed Oblivion because I'm still hunting down the last three Ayleid Ruins! Some sandboxes go for size too and end up making a bigger map than they have interesting landmarks to go into it. Fallout New Vegas suffered from this (however I don't feel Fallout 3 or Oblivion did). Saints Row 2, GTA San Andreas all had some little interesting landmarks and easter eggs, something Just Cause 2 lacked. They're all great games, the world itself it just a bit sparse in some cases.
Neither should overtake the other, that overrides variety. Sandbox dominates gaming and we'll be asking for a cover based shooting system again soon. Why not mash the two together? Just Cause 2 almost managed that perfectly.
