In the famicom version of Super Mario Bros. 3, if you got hit you turned to small mario no matter what item mario was using
In the NES version of Super Mario Bros. 3, if you got hit, you only turn to small mario if you are hit as big mario. If you're a fire mario, racoon mario or else you turn to big mario.
They're still considered the same game
I don't think the fact that you have the option to scroll faster in SMB2 makes it a different game than Doki Doki Panic
Those are considerably different things. Its not like Japan later received a version of Mario 3 called Super Mario Bros. 3 USA. The reason is that one fact alone isn't a big deal. Doki Doki vs. SMB2 are quite different. Obviously the skin alone is reason to sell it again in Japan later on. But being able to run fast does change the game significantly, certain shortcuts can't be achieved like they can in SMB2/USA on Doki Doki. I almost always played as Luigi because of his speed when running. I've played Doki Doki and its just so slow that I can't play it for very long. Obviously its not a completely different game, but its different enough for me to differentiate between the two.
Anyways, the reason the Japan VC received Mario USA before we've received Mario 3 which was already out there, is because they want to release the Mario games in the proper orders for their region. We weren't going to get Mario, then the Lost levels, then Mario 3, and then Mario 2, that just wouldn't make sense to those that don't know about the history of the game. So naturally we had to wait for Mario USA to get released in Japan first, and we'll receive it soon as Mario 2 obviously, and then we'll get Mario 3 soon after. (I totally called this in a different topic on this forum a couple months back).