Yeah... I agree. I was anticipating Darknuts, Iron Knuckles, and after the land-based Octoroks caught my eye, I was hoping to encounter a lot more of the enemies from the 2D/old school games like A Link to the Past. However, it seems to me that Skyward Sword ditched some enemies in favor of offering variety in a small group of enemies. Take the Bokoblins for instance; there were at least four different types - archer, zombie, electrified, and normal. Meh... That's no excuse for the omission of enemies, though. After all, most of said varieties of enemies and such in SS did essentially the same thing - hit you (although there was a bit of variety.) The two types of Moblins found in SS, for example, only differed in defensive properties - iron shield, wooden shield. There was also a variety of Keese with different properties.
Overall, perhaps the reasons why some enemies were omitted has to do with how difficult it would be to implement and/or adapt them to the motion controls. This rings to mind the Darknuts featured in Twilight Princess, which hardly required motion controls to defeat, given how lackluster the controls were in said game. With SS's motion control scheme, however, their inclusion might have proved problematic.