MOS Superman wins hands down... Movie Thor can barely do anything without his hammer and couldn't even defeat two villain (Thor the Dark World) and needed help from others. Superman who is by far way faster than Thor, stronger, and his full potential has yet to peek in MOS trilogy easily take this version of Thor.
To be honest, while I agree with you about Clark not hitting his peak yet,
and he appears to get more powerful as the movie goes on, I still think Thor would be a very tough fight.
While I think super-speed would be one of the deciding factors, Thor is the better fighter, hands down, whereas Clark has to think about it before using his powers ( he actually watched the pilot fall for a second before flying out to catch him). So that would give Thor an edge.
What I think would be the biggest equalizer is aggression. Thor is going to hit first, because Supes isn't a naturally aggressive guy, unless you attack his mom, if Thor attacked Clark's mom, then it's a different story altogether. But usually, Thor would get in some good hits with mjolnir, although if Hulk can catch it in flight, Supes can too, as he's a lot faster than the Hulk.
I can see Thor getting in lightning strikes, and some really good shots with Mjolnir before Supes gets pissed off, and starts using his powers at their potential or if he can keep Thor from using Mjolnir, because without it
he has to use the subway (btw, that's how Kurse beat up Thor, by keeping mjolnir away from him, we never see Kurse take a full on blow from the Hammer, in Thor's hand, which to me suggests that it might have been powerful enough to take him down).
Maybe if Thor got supes with a surprise attack, then he'd come out on top, but otherwise......
I suppose a lot of this is based on Thor getting hit by Kurse, and Kurse chucking a boulder at him, and keeping him down -whereas Supes fights two beings of similar power, and struggles (although arguably doing better than Thor did against Kurse, sorry Thor fans, but I've seen TDW twice, and Kurse gives Thor a hammering), but as soon as its one-on-one Supes is on much more even terms, and of course, he gets hit with a train, and has not a hair out of place.
As far as Thor v Iron Man goes, I think Thor was holding back. If that fight had continued much longer, he'd have put more than a few dents in the golden Avenger. On that note, given how well Killian and the extremis soldiers do against Iron Man's army of suits in IM 3, I can't see Superman having much of a problem with him.
On a different note, I quite liked that Thor needed help to beat Malekith, because that's the thing about Thor, he rarely fights alone, he has allies.
And to be fair, Malekith was about to unleash a power great enough to
extinguish all light in the 9 realms.
Superman is a different story, he's very much a solo act for most of his adventures, except when he's hanging with the JL.
I really enjoyed TDW ( it was a reasonably close second to MOS), and still don't understand all the Thor fans who didn't like it. Personally, I always found Thor the most boring character in the Thor comics, and the movies have made him a bit more likeable, particularly in TDW.
Now if Supes had to fight Thor and Loki together or Thor and Hulk (the movie versions), he might be in serious trouble.