On the other hand, when it's Johns writing the Krypton villains origin in Action Comics Annual, the tale is very Iron Age-ish in tone and style.
I disagree. The Council was portrayed as morally dubious in the 1978 movie (they were going to banish Jor-El to the Phantom Zone if he warned other Kryptonians) and giving Zod a more sympathetic origin is not Iron Age-esque either. Lots of villains, from Dr. Doom to Luthor himself have had these types of origins. Non has also become a far more interesting character now.
Also, editor Matt Idelson declared in his Superman Homepage column that in the new continuity, he still views Clark Kent as the real personality, not Superman. That's Iron Age concepts and execution.
Everyone has their own opinion about that. I doubt there's an editorial edict stating which version is true. Personally I liked the Waid/Morrison view on the secret ID. The Donner/Johns run seems to contradict Idelson's view, and a new writer might contradict their view. That's the way things work in today's comics.
Plus, look at all the things that have returned: Kal as a non-costumed "Super-Boy" in his youth; Mon-El's relationship with Kal and time in Smallville; Superman's powers are at the highest they've been since 1986; Lex Luthor is a rogue scientist again; Bizarro World is back; multiple Kryptonians; I could go on and on here.
We're definitely in a new age. I'm sure things were just as confusing during the first Crisis and the reboots afterwards. This time DC wants to present their characters in a more mainstream way though, and that means using what's familiar to fans and bringing old concepts back. The Mercury Age, at least in my view, is old mixed with new. It's about respecting the past while also moving forward. Not everyone will like it, but I for one do.
As for DC, the most reasonable approach they can take is to make the vast majority of their fans happy, because they can't make everyone happy. Granted, being a human being, I would like them to just put out stuff I like, but it's not just about what I want. It's not about "my" or "your" Superman--it's about a universally appealing Superman (or as close to one as you can get).
Anyway, that's all I'm going to say regarding this subject. I don't have anything else to add.