1) why object to Jackson's depiction of Dwarves but not Elves? In both TH and LOTR novels, Elves are depicted as being a very whimsical, light-hearted people, but in the films they're portrayed as serious and somber. If one is to find fault with one race's portrayal, why not the other?

Yeah, I see where you're coming from, but here's the difference between the two cases, as I see it. First, Tolkien moved steadily away from the whimsical portrayal of the elves as his thinking on Arda developed and evolved. The elves of LOTR are considerably less happy-go-lucky than the elves of the Hobbit, and that trend continues through his other writings, too. So the films' more somber portrayal has some textual basis. Second, where the films do depart in portraying the elves from the source material, it is done in a respectful manner. Making the dwarves into a bunch of crude jocks strikes me as a very disrespectful decision. Just because comic relief is sparse is no reason to turn Tolkien's noble dwarves into a race of Gungans.

As for the eagles, they are hardly different from the books, but the lack of development and the very "convenient" deus ex machina that they are makes me wonder if doing the films in the proper order instead of Star Wars order might have helped things make more sense with them and perhaps a number of other points as well.

You may be right, but I suspect that, from a purely pragmatic perspective, it never would've worked. The Hobbit is doing so well, in large part, by riding the coattails of LOTR. If the production order had been reversed, I suspect we never would have made it to the second trilogy.