Drop those crutches and return to the way things typically were under Berganza, in other words. Challenge yourself to come up with creative means to challenge Superman, or simply throw villains at him who can give him a good fight without resorting to cheap, unimaginative, facile tricks. Also get rid of his need to breath in space, his inability to travel interstellar distances, and his commonly low strength and invulnerability levels. Retcon out all other Kryptonians including Zod (wish you could Kara, too), kill off, retire, or simply do not use characters like Doomsday, Prankster, Toyman, and Darkseid, and most of all, cut out the meta-fiction naval gazing bullshit. Write yourself a term paper if you want to show off your junior college chops and keep it to yourself; leave that garbage out of Superman's life.
I don't necessarily think Morrison needs to remove/reduce his weakness and vulnerabilities in order to show the character respect. In my opinion, Grant's done a helluva great job with the character whenever he's had the chance to write him, weakness and all.