Well, key points of contention:
-The planes, as mentioned, are really neglected, despite having a unique and distinct cosmology, as the planes come in and out of conjunction. Dal Quor and Xoriat, as antagonist-planes get some attention, but for all that Sharn is even possible at all due to a planar bleed, the rest are ignored.
-The Dragon Below. Now, you get to explore below the earth, and theres some mentions and sample antagonists down there, but they don't affect the overworld much, if at all. Wouldn't be all that much trouble to flesh out near surface areas and what the surface worlders are doing with it all.
-The Dragon Above. I bemoan the lost opportunity really. You have ways and means to get up to the ring of Siberys, with bound elemental crafts. You'd think some explorers would be going there. For the massive lewt if anything.
-Planar Shepherd. Cool concept, but notable for being one of the few classes that can make Druid better, MUCH better.
-Shifters. Again, cool concept, middling execution. For a people persecuted for shapeshifting abilities and the like, they really don't shift much at all. Wouldn't have hurt to have shifting being something more prevalent.
-Artificers. Concept -> Execution. The class is either mad-awesome(when you abuse the crafting rules, but thats really just the crafting rules fault), or terrible. Ditch the infusions for a Craft-Schematics business and let them make their own array of unstable, but functional contraptions! Traps! Mini and not-so-mini constructs!
-Higher level play. There ARE antagonists available on the planar, dragon or underworld levels, but none of these are given much fleshing out. How do you go take a whack at these forces when theres no detail on the matter?