For example, the setting is way more varied. From trailer-parks to suburbs to the big city to the college district to a beachy area... I don't get the same feeling of driving around a living city in 3. I don't know how the actual areas compare, but Stilwater's variety makes it seem like a much larger place than Steelport.
And really, you're going for a more absurdist take on Saint's Row, and they took out those whacky french fry cars?
Also, if you're playing 3 without playing 2, you're missing out on a lot of great inside humor.
P.S. there is a distinct lack of Michael Dorn in Saints Row the Third.