(disclaimer: not speaking officially here at all. Also I don't mean to completely crush your spirits or anything. I'm just trying to explain what the outlook on something like this appears to be right now.)
I think Runouw's main focus as of right now is Last Legacy (
specifically, Chapter 3 [more information
here], and also the
Chapter 1&2 Java Remix), or, more generally, the new Last Legacy engine in Java, which is going to be used to create both games, as well as a new and revamped level designer. Look around other places in the Last Legacy forums for more info on that, like in the Updates section.
A while ago, I think there were talks about possibly integrating LL's level designer into SM63, but I haven't heard much about that within the last year or two. If anything, just an LD upgrade would probably have been the closest thing we got to the SM63 sequel that everybody has wanted so badly at at least some point in their time on Runouw, since the LD was such a huge part of the game for most of us--honestly, it's probably a lot more important to the game's success, popularity, and just general greatness than the main story.
There was a small update to SM63 back in 2012, but the game is still around six years old now, and I feel like at this point the Runouw brothers are probably moving on to bigger and better things.
At the end of the day, I think LL kind of already filled this position... if not as a direct sequel, then at least as a spiritual successor. Runouw used their experience from creating games like SM63 and others they've worked on in the past to create LL, which has a massively updated, optimized, and expanded level designer and is totally amazing. The story mode in LL is far more original than SM63's was (basically just the generic "mario saves the mushroom kingdom, defeats bowser, and rescues peach" formula), though you can tell that it took a lot of elements from its predecessor if you look closely. SM63 definitely was awesome, and it certainly deserves a sequel, but I think it already got something much better than that: LL. And LL:NS (Chapter 2). And now Chapter 3 (name pending?) is in the works, expanding upon SM63 as well as the first two LL games, as well as being coded in an entirely different language, Java, so as to fix a ton of issues and make the game even better than it would have been in Flash. If you haven't already, I definitely encourage you to look through to LL forums and read the update posts by Runouw, lulzaraptor, and -BY, as they're the main people on the dev team that actually keep in touch with the community.
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tl;dr: There probably won't be a direct sequel, sorry. Despite its awesomeness, SM63 is pretty outdated at this point, and the whole Mario fangame idea isn't nearly as fresh as it used to be. For one thing, there's not much need for a sequel, as what we have now in SM63 will probably do fine--but along with that,
we already have one. It's LL. It's bigger, better, faster, more original, more interesting, and more capable than SM63 ever was or could have hoped to have been, and it's constantly evolving.
tltl;dr;dr: No sequel. Only LL now. GET HYPED FOR CHAPTER THREEEEEEEE
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EDIT: Oh yeah. Also, at one point in 2013,
Runouw received a Cease and Desist note from Nintendo about SM63 and violation of copyright. While nothing really actually came out of that on Nintendo's part, Runouw directly said in response:
Runouw, July 13th, 2013 wrote:I am not saddened by this event, instead I'd rather see it as a chance to move on and keep working on my own intellectual properties. The release of Last Legacy is drawing near and that is my main focus for now.