At some point during the past few years, the word "linear" became a bad word in gaming. The completely ludicrous sales of the Grand Theft Auto III, GTA IV, and everything in between probably contributed to this but whatever the cause, developers are now obsessed with giving players freedom. Open-ended gameplay is a good thing in theory because allows the player more control over his gameplay experience but the concept is so badly executed in many of these so-called "open-world" or "sand-box" games that it makes me long for the days of choice-less side-scrollers.
The main problem is that developers focus on giving players lots of choices but no meaningful difference between those choices. If there's fifty dungeons throughout the world of Elder Scrolls IV: Oblivion that I can visit but they all look the same, have the same sort of enemies inside and contain similar treasure, is this really a choice? It's like choosing between slices of bread in the same loaf. I'm just going to go to whichever dungeon is closer or is located on the way to one of my main storyline objectives.
After I clear one of these dungeons, what's my incentive to clear another one? More treasure or experience points, sure, but the amount of either you can potentially attain by clearing every dungeon in the game vastly outweighs the amount you'll reasonably need to finish the game. Oblivion and a few other games even give you the option of playing after you've finished the main storyline. What's the point of getting better equipment or hoarding more gold if there's no goal to speak of? The only incentive at this point is entertainment for its own sake but generally this is reduced by the fact that most of these open-world games merely copy and paste the same content over and over across the map. Studios might boast about their game having over a hundred hours of potential gameplay but the vast majority of players will be bored silly with the game before they play the game even half that amount of time.
Another way to state the problem is that developers focus on choice rather than consequences. If I wipe out a guard post in Far Cry 2, does that affect me or the wider game world in any fashion? In the case of Far Cry 2, no, it doesn't - the guards will respawn as soon as you leave the area. Likewise, shooting a group of rival gang members in Grand Theft Auto IV or killing an entire camp of raiders in Fallout 3 will simply result in them respawning, thereby removing any consequence from your deed other than the generic incentive of getting equipment off enemies' corpses or earning experience points. Even if enemies didn't respawn in these games, the only unique result from killing them would be that you don't have to fight them ever again. Nothing about the game world actually changes.
Consequences are exactly what the main campaign quests or the best side quests add. Western role-playing games like Mass Effect or Fallout allow multiple solutions to quests and give the game a moral dimension. If you're bargaining with a black market merchant and learn that he owns a slave, what will you do? Pay him for the slave's freedom, slay him and escape with the slave in tow, or just walk away? You're able to make choices that not only give different amounts of material rewards but also change the game world. The slave is free/chained and the merchant is dead/alive depending on your actions.
The thing is, these effects are limited. Sure, you might get a quest from the slave to bring her back to her old hometown and when you arrive her parents will give you some money as a reward. But then what? After a quest is completed, the former slave or the family they've reunited with will thank you again if you initiate conversation with them but probably no one else in the game world will acknowledge the deed. The effects of most quests are limited to a couple characters or, at best, a town. While the first two Fallout games and Arcanum informed you at the end what ultimately happened to this person or that town in the long term as a result of your actions, usually you never learn more than the immediate effect of your actions in these games. You'll just be given some generic good, neutral, or bad ending at the end of the game depending on how you conducted yourself throughout the game.
Most open-world RPG's will give you a sort of "morality" score where you earn karma/reputation for committing good deeds or lose them for committing evil deeds, with NPC's reacting differently to you based on whether your overall score pegs you as good, evil, or neutral. However, distilling all your deeds into one score that fits into one of three categories of morality is an artificial, limited solution. Let's say you kill a hapless farmer outside a town and then later help a little girl find her dog. These negative/positive reputation effects from the two deeds would off-set and make you a "neutral" morality - but it doesn't acknowledge these two distinct actions.
Ideally, the murder of the farmer and helping the girl would both result in after-effects of some kind in the game world. Maybe the murder results in other farmers buying weapons on the black market to defend themselves, maybe helping the girl results in...I don't know, the dog mauling her? The point is, your actions in both cases had a noticeable effect on the world. Making a world where every little action has an actual consequence (and those consequences have consequences, etc.) is obviously really tough to code but this concept is why the idea of open-world gameplay appeals to players so much. It's nice that the game world you built takes two hours to walk across, has a 24-hour day cycle and has a hundred dungeons for us to explore - but unless we're given some ability to affect this world, what's the point?
If you're not willing to really put forth the effort to make your game's "open world" as rich as it needs to be in order to be effective, why bother making it a sandbox game? Assassin's Creed could've been a completely linear game, with players being automatically transported from briefing to mission and it honestly wouldn't have lost anything. The time spent laying out extraneous villages and countrysides between objectives could've been better spent enhancing the main missions. There's nothing wrong with a game being linear if linear structure fits the gameplay. If a developer is committed to making an open-world game, they should be focused on making their game worlds as interactive as possible rather than simply making them large or pretty.