As far as I can tell, Isaac has two major points going against him.
1) Golden Sun is a small franchise with a small fanbase. Golden Sun could easily be overlooked when Sakurai's deciding what franchises to focus on. Golden Sun isn't the only underrepresented franchise that could get a spot in SSB4. Other series like Advance Wars and Custom Robo for example have more games to their name, and might attract more of Sakurai's attention.
Compared to series already in Smash? Yes, obviously I agree. Compared to the remaining unrepresented series? Well there are still a few that have made more of an impact or are more popular, such as Punch-Out and Wii, but Golden Sun is towards the front of the pack when it comes to what's left. Other series have had more games, true, both of your examples prove this, however inclusion is not based on number of games alone, rather the impact those games have made, and the popularity of the games and characters that resonates afterwards. If this weren't the case, we wouldn't have gotten series like Pikmin, Mother, Starfox, or other games that only had a few titles to their name at the time of inclusion when there were bigger series out there that were left unrepresented. The impact Golden Sun has made (due in part to having a worldwide release for each title) does outweigh that of... really every series other than the two I mentioned and a few that have characters of questionable feasibility. And that could be what gives GS the edge, even if they aren't the top pick.
It's entirely possible that we've seen all of the new franchises we'll get, and every fighter outside of Trainer and Villager will come from existing series.
It's possible, and Sakurai clearly likes to deviate from the precedent, but it seems unlikely that all three new series would be revealed right off the bat, considering that's never been done before. I wouldn't count on the likely remaining ~10 newcomers to all be from existing series, but you're right, it is possible.
2) Sakurai plays favorites. There's no way Earthbound would have gotten as much love as it has if the series wasn't a personal favorite of Sakurai.
I'm inclined to disagree here. Remember, Smash 64 was never originally to be released outside Japan, so the character choices were likely based almost solely on Japanese popularity. At that point Mother was already quite a popular series in Japan, at least on par with like... Metroid and Starfox (who only had three and two games in their series at that time respectively). Coupled with the fact that HAL had worked on Earthbound (so there might be some studio bias, but not from Sakurai, as he didn't work on Earthbound) and Ness was likely a popular character there? A case could be made that Ness's inclusion was at that time as justified as most of the roster.
For Brawl, Lucas was quite the popular pick in Japan, and Sakurai had him planned since Melee, so once again, an argument can be made. Plus, Sakurai has stated that he personally is a fan of FE, so if any series were to get an inordinate amount of love from Sakurai, it'd be FE. But it hasn't. Well I suppose if any series were to get too much love from Sakurai it'd be Kirby, and we all know Sakurai's humility prevented the inclusion of Kirby characters other than Kirby until they were among the most wanted (and therefore perfectly justified).
A bunch of Nintendo characters deserved a spot in Brawl more than Snake, but Snake won out.
Well it's not like Snake was actually in competition with any other third-party. He's the one who broke down the gates, and yeah, Sakurai played favourites there, but one, third-parties are a bit of a different situation, and two, it's not like Snake was chosen
over somebody more deserving.
But as to how this relates to GS? Well until we know Sakurai's opinion of GS, we really can't pretend to know. He thought Isaac merited being an AT last game... but that's about it. Even if we did know his opinion, while people would probably make a big deal about it either way, I'm inclined to believe it wouldn't actually effect his chances (unless Sakurai for some reason thought he was unfeasible, which obv wouldn't happen). Sakurai adds who merits inclusion, who he thinks will make a good character, not who he personally wants to see.
Isaac has not hard arguments against him (Sakurai never called his inclusion "pretty impossible", for example), but unfortunately he's hardly guaranteed.
Yeah, I agree. While I might paint the picture that Isaac really doesn't have too much to worry about, it's hardly that black-and-white. He still has a lot of factors against him, and personally I would only put his chances at 50/50 (or 60/40 if Sakurai is compiling this roster largely off Brawl-era popularity).
