That's not entirely accurate to say with regards to Geno. He mentioned the Brawl era specifically with Geno and having an interest in including him back then. He said nothing of Smash 4. There's no implication of him trying to get Geno in Smash 4, all that he says is that he's aware of the requests and wanted the fans to have something, hence the development of the Mii costume. You're making a big jump to say the existence of the Mii costume implies a failed negotiation for Geno in Smash 4. Sakurai's quote is that, "Even though he still isn't in as a playable fighter, I made sure he'd be in as Mii costume so his fans would at least feel like they get something." All that we can actually take away from that quote is that Geno isn't a fighter in Smash and the Mii costume was developed for the fans. The specifics of why Geno isn't in Smash 4 aren't implied at all. You can choose to make the assumption that he asked for Geno and was turned down, but there's no evidence to contribute to that. He only specifically calls out Brawl and how Geno didn't end up materializing for that game.
Yes, I think Frank O' Connor's comments are the mostly definitive. He took the time to actively address the idea of Master Chief in Smash of his own accord, and as the person that has to be talked with in the event that Master Chief gets in because he serves as the Franchise Development Director and heads 343. The difference with the Sora situation is that Shinji Hashimoto was asked the question in an interview and he's under no obligation to answer in any certain way (Unless Sora's in, in which case, he cannot say yes). That's Nintendo's announcement to make if Sora is in and it's easier to outright deny it's happening until something is announced officially from Nintendo (Again, assuming Sora is in for this hypothetical). He didn't volunteer information and directly address an issue of his free will, so I do think it qualifies as a different situation from Frank O' Connor and Chief. Plus, he's the Vice President of Square Enix talking to some young dude, that's not exactly going to be the place to drop information and it's a long damn way from an official statement from Square Enix given that context.
If Tetsuya Nomura comes out of his own will and says Sora is not in, then yes, I will believe Sora isn't in. If there's a much more official venue in which Square Enix shoots down Sora, I'd be more inclined to believe it (But even then, that's still not necessarily a guarantee given NDAs still allow you to respond No to questions).
I mean he could have. Again, we don't know in the least bit. But I'm much more inclined to believe that Cloud and Final Fantasy were the priority for everyone involved, including Sakurai himself. Geno in particular has fan support, so I think Sakurai wanted to see him included in some fashion with a Mii costume given he knew how the fan base might respond if nothing Geno related came up. He was the Mii costume because of his popularity in the Smash community, and they didn't go beyond Final Fantasy content for other series too. The Square situation is certainly strange, but they've also got the most complicated rights and expenditures with regards to IPs, and I suspect Geno was likely one of the cheaper options for a Mii costume anyway. We don't really know why we've gotten so little content from them. But I do think when Sakurai has spoken of the limited resources available for DLC, it makes way more sense to go with one character in mind and he seems to have clearly stated that representing Final Fantasy was a big deal to him in Smash and that Cloud was a way to make lots of people happy. There just are limits to how much he could do with DLC, so I really do suspect that they only ever had one candidate on the table.