Many action cartoons have multiple ideas going on in one episode. And most of those things aren't major subplots that each require their own episode.
Iron Man's magic vs. science technobabble is something he'd frequently espouse in multiple Earth's Mightiest Heroes episodes as well.
EMH did this well though, that is the difference. Throughout the first season Tony would make comments that showed his frustration with magic and Thor would comment alluding to his mistrust of technology. Then they had an episode (Casket of Ancient Winters) where science vs. magic was the focus.
The sense I get from AA is that there is no overall vision or bible for the show. It almost seems like as they are going along they are picking an antagonist and then glomming on some stuff about the Cabal and maybe some subplot within the team, add in a jokey scenario and boom, episode. The show is okay but just not high quality yet.