I think the problem with sandbox games is simply that they try and be too story based in what is supposed to be a freeform setting. Story missions are important, but they shouldn't be quite as dramatic or "apocolypse looming over your head" all the time to make going out and doing your own thing seem inappropriate under the circumstances.
Time limits don't appeal to me, because in games like "Dead Rising" they generally mean I can't do what I want to and explore how I want to, without losing the overall game. Arbitrarly losing all of your hard work is also a "no-no" IMO because it defeats the entire purpose of the game, and if I know that's coming, I'm not going to be motivated to put in the time and effort.
To be honest I think current game designers need to look back to what older game designers were able to do. For example in the old "Crusaders Of The Dark Savant" game a big part of the game revolved around trying to find a bunch of maps that when linked together allowed you to get to the Macguffin the game revolved around. The thing was that there were other factions looking for the same maps, and a timer of sorts in place, if you spent too long faffing about (as Yahtzee put it) one of the other factions would take it, and then you'd have to find the proper NPCs (which themselves moved around, searching) to get it back, which could involve killing them or buying it depending on what faction they were in relation to who you allied with (or you could just kill everyone if you were a complete sociopath, but desicians like that could impact the ending and how the sequel began if you saved and transferred your data).
I'll also say this entire "Jetpack" fixation is starting to annoy me. I understand why a lot of people want them, but all of those reasons are also a big part of why they aren't something likely to be implemented heavily. Simply put, being able to fly over the content tends to ruin a lot of it, in a sandbox game you no longer have to really worry about the police, traffic, etc... in Morrowwind being able to fly basically meant that you could ignore everything except the jillions of cliff racers if you were so inclined. Flying in a lot of games pretty much reduces a lot of the challenge to zero, and also admittedly cuts down on gameplay due to reduced travel times, and requires a lot more work to make sure everything looks smooth from above, where things can be more easily hidden from a ground based player. Unless your point is to trivialize a lot of the general world content (like in a lot of super hero games) and want to retain the challenge, it means having to design with three dimensions in mind. To say make a crime game as challenging if you jet pack from place to place, you'd pretty much have to put thugs with rocket launchers or whatever on every building, or greatly expand the number of air based enemies (police choppers, etc...). In some cases this could really ruin the vibe, especially if you plan to make your game seem at least partially serious.
Likewise, flying would kind of ruin a lot of those collection quests where half the point is to make people jump into awkward places. A good flight system that retains the player's abillity to act normally, kind of makes jumping and related puzzles and challenges irrelevent.
Opinions vary of course, personally I like being able to fly in games (so don't misunderstand this) but I understand why we don't see more of it, and I think a lot of gamers need to understand that, as well as why such abillities if they exist tend to be VERY late game OR limited to specific sections that are built around them.