Okay, here's some of my views based on these points. I would have gone much longer on this and made more sense because I feel this is just my blathering on another BluePikmin thread, but right now, here's where I'm at:
*Golden Sun: If there is a Nintendo IP that is the epitomy of the "have nots" for Smash Bros., Golden Sun is at the top of a lot of people's lists. To me, the problem with the franchise is how perception becomes reality. Dark Dawn, which was released in 2010, had a good reaction and sold fairly well for second-tier IP standards for Nintendo, but because there were some negative responses towards certain parts of the game, the idea that this was a terrible game suddenly took over, and possibly broke the confidence level Camelot had towards the franchise and also Nintendo's focus on the series.
However, that doesn't mean they are abandoning them entirely, as it appears that Golden Sun is a mainstay in VC sales, meaning there is still interest in the franchise. But, right now, it doesn't look very good for the series. When fangames seem to take more interest in satisfying your basic requests while the commercial entity doesn't even bother giving you a consolation trophy on the portable version, it is disenheartening. In retrospect, if Isaac was formally announced as an AT during last year, it would have been a lot better than waiting... and waiting... and waiting... and discovering Golden Sun's only new contribution was an original track in Sakurai's Favorite Stage.
And it also is rather strange how they decide, in a time where resources and manpower was pushed to their limits, they removed an easy AT for some very complicated (and a few even more obscure) ATs, as even Dark Dawn's ills shouldn't have been that horrific. Yes, yes, "relevancy", but I'd rather throw the bone than decide "Nah, not gonna bother".
*Personal Bias: Sakurai has personal bias. But, so do we all. That's why there's a lot of Uprising crap in this game, why Palutena and Dark Pit are playable, and why Medusa is reduced to nominal status in spite of her having the criteria of being a "retro" character. And, yes, I know I've said I hated Uprising, and I still stand by that, but this was because I was so dissapointed and irritated at the game when I finally did play it and not any personal ill-will towards Sakurai himself.
I mean, I believe that there was some motivation in his decisions because he's in charge. I mean, some of us want to condemn him, but at the same time, he's still a human being.
*Is Sakurai Honest?: Sakurai isn't exactly honest with his opinions, and I always dubbed him "a cryptic man". But, in his quest to avoid infuriating people, he winds up infuriating them instead by refusing to explain his true motivations. For example, SSB4 doesn't have a true Adventure Mode because he hates the Internet. In reality, given how much time the games had to have had resources thrown at them, you couldn't really do a full SSE-type mode... although you could still do a basic Melee-type mode, IMO. He's also never going to mention who was not considered or who was abandoned for these same reasons.
*Relevancy > Demand: One thing I get irritated about is that SSB is about celebrating Nintendo's past, not the future, yet I always find people who argue otherwise. While it is easier from a promotional standpoint to use a character who appeared in a marketable game, that doesn't mean that it's the only criteria required that makes or breaks a character. I still think that Nintendo would be wise to consider one to three Demand > Relevancy characters, primarily because most video gamers have very good memories, and at the same time, they should treat with caution with releasing Inkling as a playable character, should they decide to go that route.