I wouldn't mind hearing your theory. It might not convince me that Isaac still has a chance at becoming playable in smash, but I'll still hear you out nonetheless.
So this mostly hinges on Isaac's perceived popularity in the Ballot, but here goes:
THE GREAT ISAAC IN ULTIMATE THEORY:
Let's establish one thing: Ultimate looks rushed. Some models look bad (Isaac), some strange choices were made (Chrom's still in Robin's Final Smash, what?), and in general the turnaround from Smash 4 was crazy. Sakurai had like two years to finish this game, as opposed to Brawl or Smash 4, which each had a longer development time. With the focus on bringing back vets and fan favorites, Sakurai realized Isaac was popular enough to warrant inclusion, but he couldn't be finished in time, as his Psynergy attacks would take up too much development time. So, Sakurai decides he'll bring back Isaac's Assist Trophy for the time being, since he already got the rights from Camelot (not rights, per say, but permission, I guess).
Let's back up a few months to when Sakurai got these rights. Camelot has previously stated they'd make a new Golden Sun game if fans were interested, but they didn't actually expect this amount of demand. When Sakurai goes to Camelot, they're surprised at just how popular Isaac is, and realize people actually do want more Golden Sun. This is probably in Q3 (Late Summer-Fall) 2016, giving Camelot plenty of time to start working on a new game. While they have to finish Mario Tennis Aces, they start contacting other companies, like Monolith, to help them remake the first 2 Golden Sun games to get the team used to working on Golden Sun. Once Mario Tennis wraps up the pre-launch development, most of its team is sent to help with Golden Sun, but the game still needs more time, and it finally projected to release sometime (probably late) in 2019, prime opportunity for Smash DLC. Obviously, this game would line up perfectly for Isaac to be added in Smash, since it offers an excellent promotion for a revived IP, and Sakurai also gets to satisfy fans.
Fast foward to August of 2018, when most of the game is probably done (as in the characters are just being balanced, extra modes being worked on, etc.), and Sakurai tweets the infamous "Rathalos Tweet". This tweet shows three swordsmen lined up to face Rathalos in the Colosseum, and the resemblance to Golden Sun is uncanny. Link as the silent protagonist, Marth as "Mars", like a Mars Adept, and Shulk as the future-seeing Ivan. The tweet couldn't have been just a coincidence, as it's impossible to line up the characters like that in a normal match. Not to mention, the battle in the Colosseum is reminiscent of the Doom Dragon battle at the end of Golden Sun, against a giant dragon in an arena. Now, at first, the Isaac community (myself included) believed this to be a sure sign of Isaac being in Smash. However, this was not the case. Some say the tweet is a Monster Hunter reference, but I think differently. (This part doesn't come from me, but I
think JaidynReiman brought it up first) Back during the Smash 4 hype cycle, Sakurai tweeted a picture of the Monado, and lo and behold,
exactly one year later,
to the date, Shulk is revealed. I believe the Rathalos tweet wasn't something of "Hey, check this out! This thing is in the game!", but rather, "Hey! Check out what we're currently
working on!", as DLC would have been started to have been discussed right about now.
This brings us to the present day. Isaac's revealed as an Assist Trophy, and we're all sad. However, do not fear! Sakurai confirms that
Nintendo decided DLC, not him. This is good news for Isaac's base, as Nintendo might be more willing to not only give fans what they want, being directly on the receiving end of requests, but also to promote any upcoming games. As it so happens, one of these upcoming games is a new Golden Sun, and Nintendo can see the dollars rolling already. They realize they can basically double dip on Isaac's popularity: Not only will nostalgic fans buy him and the new Golden Sun, but his inclusion in Smash as a brand new geomancer will make casuals interested in Isaac as a character. Now Nintendo can say "Hey, you like this Isaac guy? Check this out: it's the game he starred in! And it just came out! Crazy, right?" This will help to ensure the Golden Sun remake sells as well.
I have a bit more evidence to add that doesn't really fit anywhere else: Isaac's model doesn't look great (compare it to other Assist Trophies - it looks pretty bad, especially with the sleeves and face), giving evidence to my theory that he was added in last-minute to please fans, and not to mention when Isaac was shown off in the Direct, they used the
Felix Battle Theme that's been around since Brawl. Brawl! He was the only Assist
not introduced with new music, which is quite strange, huh? Maybe they're saving it for a Fighter Pack with Isaac?
That's my crackpot theory on Isaac's chances in Smash. I've managed to completely convince myself, but I give it around a 5% chance of actually happening. Mostly, I'm banking on Camelot realizing the demand for a new Golden Sun and Nintendo wanting to promote characters with Ultimate's DLC. What do you guys think? (Also, KMDP, feel free to remind me of anything I missed, since most of this comes from the Isaac thread.)
EDIT: Holy crap, I forgot all about the trademarks! In August, Nintendo trademarked "Golden Sun" in Japan, different from the usual 「黄金の太陽」trademark usually used. This leads me to believe that Golden Sun will be relaunched worldwide as "Golden Sun", creating a single, stronger brand.