Here's my hypothesis: In Hulk #3 Kirby had the Hulk gain new powers thanks to cosmic radiation (the same way the Fantastic Four got their powers) and Lee overwrote it. I think this comes from Stan Lee objecting to characters flying for no reason. Few characters could fly in early Marvel.
(Personally, I wished writers were more discriminate with flying power. I don't know what would be the wind force necessary to fly a human being and the amount of noise it would create but I wished X-Men didn't speak in mid-air when flown by Storm. To this day I'm annoyed when I see Sub-Mariner carry people when he shouldn't be able to fly. At least his 70s costume made it likely he could glide.)
Many panels in Hulk #3 to #5 show the Hulk flying, not leaping. It’s only the text that says he’s leaping. There’s not one panel that shows him unambiguously leaping while there are several that show him unequivocally flying (he changes
direction mid-flight, turns right or left, takes off like a plane):
#3 page 24
#4 (first story) page 6, 9
And every time you have Lee captions which explain it’s not flying. Coincidence? Hardly.
The second story of #4 page 6 is the first panel where he is shown clearly leaping but that’s a different, smaller leap to create a shockwave to scatter soldiers when Hulk hits the ground.
On page 9 the panels are more consistent with leaping long distance.
It’s only on #5 second story page 1 that he rebounds.
Clumsy as the overwriting looks, I have to agree with Lee's instant retcon (just editing actually). It makes the Hulk more interesting. And it worked.
To this day some people have said Hulk wasn't flying in those issues so Lee must have been convincing. Like many I read those early Hulk issues after I had seen him in later Bronze Age issues so I also didn't think he was flying when I first read those early issues.
Since a picture is worth a thousand words, look at those trails...
The panels unequivocally show the Hulk flying and thus an intent on the part of the penciler for him to fly. Just as well the captions go at great lengths to overwrite the visual and show an intent for the Hulk not to fly. And this in two stories, Hulk #3 and the first in #4.
My guess is that Kirby was already at work on #4 before Lee informed him of the changes in #3. It also suggests that Kirby was doing a good part of the plotting already in 1962.
(And maybe earlier if someone gets to analyse and compare the various versions published by Atlas-Marvel of the same stories. Lee was known to submit an old plot when he didn"t have a new one ready for a penciler.)
There is a possibility that Lee first asked for a flying character and then changed his mind at the scripting stage but I doubt that.
Kirby was the one who made unlikely characters fly (Thor) while Lee strived for more realism.
I don't have my Omnibus at hand but I think it's Kirby who added the bootjets to Iron Man.
In recent years some pages of a rejected Hulk story have surfaced;
This wordless story seems to show the mental link between Jones and Hulk that was established at the end of the first story in #3 and that Hulk received along with the flying power.
So, were those rejected pages supposed to come in issue #3?
Issue #3 retells the origin in three pages. It's a bit odd so soon after the first issue to do that. Then the Ringmaster is a character from Kirby's run on Captain America Comics. Did Kirby come up with that story in a hurry? The last page shows Hulk not only flying but looping (page 24).
Issue #4 starts with a machine aimed at Hulk's head (page 1). Was that originally connected to his injury in the discarded pages? In that same story the soldiers train against a jet-powered robot Hulk (page 4). Lee puts a lot of effort in his captions to explain that the Hulk leaps in such a way that he seems to be flying (page 5).
In #5 there are still many panels where he seems to fly (1, 3, 6 -cf the twisting trail as he leaves the plane-, 7, 11, 12, 13). On page 1, 6 and 12, we have rebounds and I wonder if these weren't added/redrawn by the inker at Lee's request.
It is known that Kirby generally didn't read the pages after Lee had scripted them. Was that why the flying Hulk went on for so long?
Or was it a disagreement which led to Ditko taking over with issue #6?
Ditko's Hulk is more clearly leaping. Page 2 is ambiguous but page 3 is less so. On page 8, no place is left to any doubt with the Hulk bracing and bending his knees in slow motion.