I still think it was worthy of a nod, though again, "Kong" was obviously the choice to win.
I dono, you know how academy voters like to award the last movie in a series by voting for the series it self and not the movie. SW EP3, if nominated, probably would have won due to all the people voting in that category rewarding Star Wars itself and not necessarily ep3.
As for which one was better, ep3 or Kong, that's a hard one to choose. I don't think EP3 was as video gamey as Ent is saying (attack of the clones defiantly was though) since all 3 prequels have had that every thing's shiny look which I think was done on purpose. In the original 3 things are run down and give you the feel of how desperate the Rebellion is and how much the Empire has choked the Galaxy. In the Prequels you have the exact opposite to show how good things were with the Republic and Jedi.
Kong, on the other hand, had great environments and interaction with those environments. Though Kong himself was quite boring in that regard, sorry I just expect CGI characters to looke that good so there was little wow factor there, plus he only interacted with a few non-cg things.