Honestly kind of amazed my initial post-Direct reaction is already over 10 pages back. Clearly there's been a lot of talk over the implications of this Direct, so I'll go ahead and throw in my two cents.
First off, Isabelle's inclusion: the second the trailer started up was an "Oh, duh" moment for me. Not only was she a character I expected to be included, but she makes perfect sense in a regular Direct alongside an announcement for Animal Crossing Switch. Maybe she doesn't excite the normal Smash crowd, but she definitely excites more casual Nintendo fans, and I've already seen some extremely positive reactions on Facebook to prove it. In retrospect it feels natural that she'd get revealed now as a bit of cross-promotion and not in our expected second Smash Direct, which can instead be reserved for characters that really excite the core audience like K. Rool was the previous Smash Direct.
Second, implications for Isaac specifically: frankly, nothing has changed. Again, Isabelle was an expected inclusion, and it's good to see she was made a semi-clone so as to take the minimal number of development resources. I think that bodes extremely well both for the potential number of unique newcomers left in the base game as well as the potential number of echo fighters and semi-clones. I also don't see an issue for Isaac in terms of reveal schedule, as it would make a lot of sense for him to be reserved for a Smash Direct where more of the viewership is likely to know him and where there should be other exciting reveals in store for those who may have never even heard of Golden Sun. We also can't discount the possible hints we've seen like the conspicuous Rathalos screenshot and the recent Golden Sun trademark renewal. The only real downside is that he hasn't been a part of the increasingly credible Vergeben leaks so far, but even they don't claim to know the full roster. In my view, Isaac's chances remain strong, if admittedly far from guaranteed, and nothing today has changed that.
Finally, a note on the Isaac fanbase. If there's one thing that has become clear today, it's that the desire for Isaac in Smash is very real and very public. It's not just this Smashboards thread, but people on Twitter, Reddit, and even Twitch chat that are talking about our golden boy. Perhaps Isaac used to be a longshot, but if this kind of public interest keeps up, we could very easily see him as part of the inevitable DLC lineup should he miss the base game. Further, this is exactly the kind of enthusiasm that Nintendo is liable to notice and thus may encourage Golden Sun ports, remasters, or even brand new games. I know many of us are disappointed today, and I'd be lying if I said I wasn't as well, but this isn't the time to give up or assume the worst. If anything, now's the time to double down and prove we're in it for the long haul. After all, that fan effort paid off for Ridley, and it paid off for K. Rool. We're one of the biggest remaining fan requests still going, and if we're willing to stick with it, I have faith we can get the reward we've all been waiting for.