Cfrock
Keep it strong
The Hyrule Historia does say this as well though, a little bit before that quote:
While this doesn't prove that Daphnes stayed behind out of loyalty, it doesn't support the idea of him only existing because he was summoned by the Gods. This quote makes it seem more like the Gods chose him to stay behind, either to guard Ganondorf or, perhaps more likely, because they knew he would be needed in the future.
Getting on-topic, I rather like this theory. It follows a clear logic and I can't see any real holes and, as such, there's pretty much nothing I can add to it. The opposition to the theory seems to come from the notion that the name "King of Red Lions" is exclusively linked to the boat itself and not the King of Hyrule. But, as the theory clearly states, even that is accounted for by the King's need for secrecy on The Great Sea as well as the evidence which suggests the boat was purpose-built as a vessel (wink wink, nudge nudge) for the King's spirit. There are no other boats like it anywhere in the world and, while there is the possibility that the name may be specific to the boat, someone had to give it that name, and who is more likely to do that than the man who will be the boat?
There was also the point raised about the boat getting the name because of how it looked.
I've never really felt that it was worthwhile to argue the point of what the boat looks like because it seems to be a fairly subjective point. I don't mean to draw specific attention to Wolf Sage, he just had the most apt quotation to demonstrate that one view is that the boat looks like a lion. I myself have never once thought the boat even slightly resembled a lion. As Dragoncat said, lions don't have horns. The boat's long neck also doesn't speak of lions, nor does it's mouth with the flat 'teeth'. I've personaly never thought there was anything even remotely lion-esque about the boat's appearance. When I first played the game I thought 'dragon', due to the horns and neck, but even that never seemed like a good fit.
Once I met King Daphnes it all made sense to me. The boat looks like him. They have the same eyebrows, the same nose, the same mutton chops. Their eyes both have the same expression in them, they have the same basic colour scheme, and the boat's horns resemble the King's crown. As soon as I saw the King, it clicked in my mind that the boat was made in his image, which made sense to me since the boat is him. In light of this theory's proposal, that connection seems more clear and deliberate to me now than it ever has. Of course, like I said, what the boat looks like is subjective. It can never prove or disprove the theory, only influence if you agree with it.
Another point that came up was why use lions to symbolise the Sheikah? Locke brought up heraldry to demonstrate that the name was simply a direct reference to Daphnes being a king, but then why "King of Red Lions"? As was already discussed it doesn't make sense and heraldry typically tries to avoid redundancy; everything has its meaning and doubling them up just wastes space. I would doubt the "Red Lions" is only an heraldic reference but I do think it is partially responsible. Lions in heraldry tend to denote royalty and they have done for a really, really long time. So long that it's ingrained in the public consciousness. You hear lion, some part of you thinks "king", even if only the phrase "King of the jungle". The connection is there and we learn it at a fairly early age. Disney very directly gave an entire generation a reason to connect the two words back in '94. So the "Red Lions" part does most likely come from such associations but, due to the redundancy of "King of Red Kings", I find it more likely it is simply due to that cultural connection of lions and royalty rather then specifically to herlads.
The Sheikah are also connected to royalty. It's not often that the Sheikah are brought up in-game but when they are there is usually a reference to their role as protectors of the royal family not far behind. In the world of Hyrule, the Sheikah are intimately linked with royalty, just as lions are symbolically in the real world. It's not really a stretch to presume that lions would be a pretty appropriate symbol for the Sheikah, even before factoring in the associations of pride and courage and protection as well.
I have to say though, my favourite part of this theory is the parallel drawn between King Daphnes and Princess Zelda's actions in Ocarina of Time. As Blue pointed out, The Wind Waker makes the strongest attempt of any of the games to connect with the lore of OoT and having two members of the royal family hide from Ganondorf by assuming the guise of the Sheikah is a really good way to do that. The theory made a lot of sense and I was nodding my head along to it, but that was the part which convinced me.
