I honestly had no idea what Endless Ocean was to be frank, I had to look it up just now. But having said that, I think the reason is likely just that people mostly focus on characters and it doesn't look like there's a ton to pull from there. However, I feel like they could make an amazing stage based off of Endless Ocean. It could be beautiful!
As far as Conker goes, that one seems pretty clear to me actually. I think most people, myself included would love to see both Banjo and Conker in Smash, but I'm not going to lie and say I think getting both is even an option. Getting Banjo alone isn't guaranteed. So I think people just gravitate towards the character they want more and/or see as the more likely candidate. And frankly, as much as I love Conker, Banjo was definitely more iconic to Nintendo during the N64 era than Conker, especially for those that couldn't play Bad Fur Day due to the rating. I think Banjo is just more iconic, so when faced with a perceived choice between the two, people are likely going to go with Banjo, even if they like both options.
As for Spyro, I can't speak for anyone else, but while i love Spyro and would love to see him in Smash I still heavily associate him with the Playstation. Which, while not disqualifying him, makes him feel both less likely and less fitting. I would personally like to see characters liek Banjo, character that I heavily associate with Nintendo, before gaming icons that I don't (even if I also love them). I wouldn't be mad about Spyro making it, but given the choice between the two I would choose Banjo every time.
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As for my own answer, I have to say Bomberman. I would have personally expected him to be one of the premier choices for a 3rd party candidate and that simply wasn't the case. He definitely had a fair amount of support, but in relative terms not huge like I expected. It just feels like he hits every category. He is absolutely iconic , he has heavy ties to Nintendo, he has immediate relevance being one of the few franchises Konami is actually using right now, and he has moveset potential given his adventure games (even if people get stuck on the whole, but all he has is bombs thing). I think his problem seems to be that while people support him, he is few people's favorite, combined with his perceived lack of moveset potential.
There is also definitely the possibility that Konami itself preferred a different character be included for whatever marketing reasons, but we obviously can't comment on that.