Edge magazine just did a Time Extend feature on Crackdown, causing me to be overwhelmed with nostalgia and haul it out of The Pile. I'm running through it again and finding that as a pure game I'm enjoying it more than Assassin's Creed 2, InFAMOUS, or Uncharted 2 (let's call them the Big Three). Those are all great games - I played them all twice (which is rare) and enjoyed them immensely. Their production values certainly eclipse Crackdown's crudeness.
But Crackdown has one advantage they don't have - an irrelevant plot. Allegedly this is just because Realtime Worlds ran out of time and money, but it doesn't really matter. Crackdown delivered the epitome of a sandbox game with these very important characteristics (some stolen right from the Edge article):
Points 1 and 2 are particular sticking points with the Big Three. They can't let you progress too fast because they have an arc of progression plotted out and a story they need to tell. Their stories also demand a certain level of realism (as strange as it feels to say such a thing about games like Uncharted 2 or Assassin's Creed 2, but a good universe sets credible parameters and sticks with them). You can't credibly have Nathan Drake dangling off signs in fear of his life if he can bound over entire city blocks.
Assassin's Creed 2 is particularly constraining here - at least by the end of InFAMOUS you're doing wire slides and using static thrusters to glide from rooftop to rooftop. But Enzio is still stymied by middling sized streets - he can't jump any further than he did at the start of the game, even though you've done it a thousand times. This is 'realistic', and having him bounding halfway across a city would be surreal, but it's still a frustrating imposition of the plot and setting.
All of the Big Three suffer hugely in comparison to Crackdown on point 2. Collecting items gets you meager rewards, but mostly are just there to satisfy your instinct for completionism. I admit, I never collected all of everything in any of the Big Three. Nothing is as compulsive as those Agility Orbs in Crackdown, which make you better at collecting more agility orbs. What's the reward for collecting flags in Assassin's Creed 2? Not a damn thing, unless you get all of a single type, and even then... meh. Treasure chests are useful early on, but before long you'll be swimming in cash anyhow. Uncharted 2 gives you access to interesting bonuses (as per Ratchet and Clank), but are mostly just completionist and self-referential in nature.
Finally, points 3 and 4 are the biggest traps of all (perhaps we could add Grand Theft Auto IV in here). Crackdown can let you do what you want when you want to do it because there's really no plot to subvert. The others, particularly Uncharted 2, are intent on telling a story - Uncharted 2 really does feel like a playable movie.
However, as good as Uncharted 2 was, I don't have any moments that are as spectacular in retrospect as some of my moments in Crackdown were. Every time I did something awesome in Uncharted 2 I was pretty sure that it was designed by somebody else. The second playthrough pretty much cemented that. I didn't do that, it was pre-ordained. Especially the fourth time through that bedamned dangling train - the magic was entirely gone and I was just sick and tired of crawling up the side.
On the other hand, I still remember clawing (leaping?) my way to the top of the Agency Building in Crackdown, then jumping off. I remember driving my SUV right up the side of a building and launching myself off the peak. I remember stacking bodies around a pile of barrels and setting one of them off. I remember harpooning an enemy to the side of a vehicle, attaching a proximity mine, and sending the whole thing careening into a bunch of goons. I remember throwing bodies at random cars, just because you can. I vaugely remember the end boss fight, but it really doesn't resonate; The best bits of this game are the bits I designed for myself (or think I did). Most importantly, I still remember things I did in Crackdown three years ago while most of Uncharted 2 except the annoyances are just fading into haze.
I am not going to say that Uncharted 2, InFAMOUS, or Assassin's Creed 2 were wrong to want to tell a story - and it seems most people are most comfortable when guided, so perhaps this is the safest and most profitable approach.
However, there does seem to be a compromise between these extremes. As demonstrated in an JRPG series of all things - just about the last place you'd expect such freedom. I'm talking about Chrono Trigger and Chrono Cross, of course. They're fairly linear, but also allow for some radical departures for the savvy player. If you really want, you can go kick Lavos's butt fairly soon. And unlike most games, where this short circuit would cause anachronisms, Chrono Trigger allows it and has an ending for this eventuality. Want to leave the world in the claws of dinosaurs? You can do that. I'm convinced this is a large part of the lasting appeal - it certainly isn't the tedious Millenial Fair.
So I realize that exploding complexity and time budgets are a big reason you don't want to allow freedom of choice, but the gaming moments that are most memorable are those that involve the player creating his or her own narrative - just look at the popularity of multiplayer modes, which have only the faintest of plots. Consider guiding the player but allowing them the freedom to break free if they really want to. I really don't think InFAMOUS would have been irredeemably harmed if a skilled player could get the static thrusters early on, especially on a second playthrough. You might turn your game from a bullet point into one remembered fondly a decade later.