I'll back a previous comment that "lessons were learned" for the second adventure path.
I found that Age of Worms tied together more nicely than Shackled City. There were more "easter eggs" for old-school players, more foreshadowing of future events, and a more consistent overall theme. Some of the Shackled City modules were quite out-of-place (e.g. I had players asking me in some sessions: "Why are we here again?"... "I don't get it - what has this got to do with what we're trying to achieve?"). Admittedly, that might have been DM error, but posts I've seen on the Paizo boards seem to agree ("Test of the Smoking Eye", anyone?).
I also enjoyed the variety of modules in AoW more than SC. Most of the SC path can be categorized as "traditional" dungeon modules (an extensive keyed area that you must proceed through, eventually overcoming a big challenge at the end). There were a few exceptions. Part of an early module is more of a cat-and-mouse with a nasty villain, and a later module has an emphasis on rescuing innocents. But for the large part, the modules are quite straight-forward.
AoW is a little more varied. There are battlemap sieges, arena contests, puzzles, and far more opportunities for diplomatic (or deceptive) outcomes. One memorable module in the series is almost all diplomacy, and is absolutely brilliant.
The big thing that sells me on AoW over SC, however, is the effect on my players. We finished SC a long time ago. They had fun with it, but today they have difficulty remembering the last couple of modules and describe the final big bad evil boss in generic terms (i.e. they never use its real name, simply a description of what it was).
AoW, on the other hand... The "big bads" in the last three modules are all iconic figures in D&D lore. My players are currently in the midst of module 10 and are gagging for a chance to take down a certain creature from a very old 1st edition module. And they are actually losing sleep over the big bad in Module 11 (an even bigger name from 1st edition).
In summary, I'd say: "Go with AoW", if you're looking to choose between the two. Of course, path #3 (Savage Tide) has just begun, and is looking even better than the first two...