To be fair, Geno and Isaac aren’t exactly important characters compared to the likes of K Rool, Ridley, Simon Belmont, etc. Geno is a one-off character from a spin-off game, Isaac only had a few fairly popular GBA/DS games. Banjo on the other hand was basically one of Nintendo’s icons during the N64 era. He falls more in line with the likes of K Rool and Ridley than Isaac and Geno
Golden Sun was decently well pivoted as one of the Gameboy's early and noteworthy IPs. Sure, it didn't reach Banjo's sales, but there's a decent statement to be made of Isaac being a smaller icon that Nintendo could actually put in whenever they want to. He's still representative of a different era (Though his DS game probably did the worst damage to his chances in proving that GS was inherently less marketable and successful). I'd argue he's only really a tier below someone like King K. Rool.
You know it's funny that when discussing Isaac the conversation goes that he wouldn't get in over Ridley and K Rool when the problem is he didn't get in alongside them. There's still other characters that got into the roster yet we are acting like it's expected that there should only be one or two fan characters added at a time. It shouldn't be Isaac or those two we should have gotten all three. There was plenty of space and plenty of time to add those 3 as newcomers.
I'm very aware and that's partly my point. People are content we got two popular characters but really we should expect more characters to be picked based on fan wants. But instead, we debate who of the popular characters deserved the minority of space Sakurai decides to throw our way as the rest of the roster is decided by other factors, instead of the other way around. Also, she wasn't that popular, maybe in AC but for a Smash character not really. People just accepted her because of Verge.
I'm always going to push back against this rhetoric of we have to prioritize fan requests over other characters. I've said it before, Smash Ultimate had the perfectly balanced newcomer spread. We had two popular requests in Ridley and King K. Rool, two new icons that had burst on to the Nintendo scene in Inkling and Isabelle, and two of the miscellaneous additions in Simon Belmont and Incineroar (Sakurai said he wanted to include a new third party franchise, so I kind of give Castlevania that spot). But when you look at it, Castlevania was decently well requested (Simon and Richter were both added to satisfy some fan demand AND because Sakurai thought that the whip was the more iconic part of Castlevania to represent:
https://www.youtube.com/watch?v=jmS05ZX3C4w&t=546s), Inkling was also one of the top requests, and the return of the veterans was also a major presence in regards to the ballot.
If you consider returning characters and their generally high ranking on ballot related polls, you'll actually get a much higher number than just two ballot choices: Ice Climbers, Wolf, Snake, Inkling, King K. Rool, and Ridley. That's six right off the bat at the absolute top of many polls. If you count echo fighters, Daisy, Chrom, and Dark Samus were all chosen because of ballot considerations as well. So you can pretty much count those as well. The remaining four veterans that were missing also generally managed to poll decently well, so they could also be considered "ballot picks." That'd be 13 of Ultimate's 18 newcomers in because of fan demand. Ken and Richter fall into a weird place as is, leaving really just Piranha Plant, Incineroar, and Isabelle.
Isabelle is a straightforward semi-clone that was the breakout star from one of Nintendo's most successful IPs. Smash is still about Nintendo at the end of the day, so she's hard to really deny her place. That then leaves Incineroar and Piranha Plant, which are both Sakurai absolutely flexing his creative muscles with characters he enjoyed. And there should absolutely be a place for that sort of creativity in Smash. Some of Smash's greatest characters have come from such decisions like ROB, Ice Climbers, Mr. Game and Watch, Wii Fit Trainer, and so on.
The fans were listened to almost completely for this game, and this extends well beyond characters to every facet of the game. And if we go the fan only route, you're going to miss some amazingly creative characters and ideas, as well as also just blatantly ignore up and coming characters and anybody who might have a legacy to consider in inclusion. There's room for all three types of newcomers in Smash, but we shouldn't necessarily prioritize one over the other. And Ultimate genuinely just did not have a lot of development time to work with it seems the more we look at things, so newcomers were always going to be extremely limited and they did a genuinely good job with balancing the newcomers this game.