There are other things you can do with a good story that are not necessarily combat based. It's about having motivation and stakes. Imagine a sequence like in SR where you save a plane or something using the games' mechanics. They need to have you do things while flying, having a lot more control during flight, both presenting power and agility. Keep it simple with a 'use' button that interacts while in flight. Set it up with some missions earlier that establish the ability and later make it be super technical. There are so many potential things to do if you just think of it as, what is it about Superman that you'd want to do. At the top of my list is awesome flight and the ability to feel incredibly agile during flight, combined with strength. That is one of my favorite things about that SR plane sequence, and it would be a great thing to include a Superman game beyond just fighting.
There are ways to make a good Superman game, but it comes from story and motivation not just action elements. And there's also the possibility of having great Clark stuff, using his investigative journalism for clues to save Lois or something. Having a section where you need to use your powers as Clark but without being seen. Tons of stuff to make it a uniquely Superman game, with a good story anchoring it. And all of Superman's villains use things to fight him (Lex builds machines or employs other people like Metallo, etc.) It just has to feel connected the way that the Arkham games bring in cameos that feel completely warranted.
I also didn't read that Rocksteady interview as them saying it's not possible to make a good Superman, it's just not going to be able to use the same formula that makes their Batman games a success.
EDIT: Nathan, I see were thinking along the same lines here. Not to mention, how cool would it be if the story begins as if the villain is Luthor/Metallo, only to have Metropolis slowly have more elements from another dimension as we realize Darkseid is behind all of this, trying to bring Metropolis into his dimension (or something, haha, I have no idea if he's ever done something like that, but it seems like he could and would). So now we can bring in true beings to combat him that are not just robots. This is just a quick write-up but I'm sure there are tons of sweet possibilities. Just make it a layered plot that keeps you (and Superman) guessing, as you try to figure out what's actually going on in Metropolis. In the meantime, obviously Lois gets kidnapped, yadda yadda.
Another great thing that Arkham does is constantly up the ante. So at first, as Supes, you can just walk through bullet-fields, knocking out thugs as you go by, but later they start using Kryptonite as a way to slow you down, so now you need to dodge these bullets, or they use kryptonite dust or some **** in the air to keep you from doing certain things. The idea of progression from your enemy is key to making them feel real and a threat.