Ugh. Well, let me start by pointing something out. The reason that just about every single one of these things is being regarded as a completely bad thing is because of how the game is now. While you can argue that you wouldn't have liked the game as much, I can pretty much guarantee you wouldn't have been horrified, because you wouldn't know any better.
That said, I'm actually not that bothered by the idea of any of these. I don't think any of them would have made the game suck. I
am glad that it turned out how it did. I wouldn't trade Ocarina of Time how it is for something else, but none of the ideas are bad, really.
Within a single castle? I came up with a Zelda fangame idea that was similar, and really honestly, if you still had a Zelda-like open world WITHIN a massive structure... that's just a fascinating idea. At least for one game, I don't see how one could consider that a bad thing. Especially when you think about how they would do dungeons and different environments within the castle. The creative possibilities are awesome. Besides, this is basically what Metroid does. Metroid nearly always takes place within a single cave network or space station, with rare exceptions (mainly in the Prime series).
Lon Lon Ranch burned down... that only sounds bad because of the ranch how it is now. I don't like the idea as much as having the ranch intact, but it's not an inherently bad idea. Would have been interesting. As for Hyrule Field disappearing? Well, I was never a big fan of Hyrule Field, so I don't think it would make that much different for me personally. The Epona gameplay on the field (for the most part, the only place where you get to really use her) is not compelling, at least for me, so she's mostly fast transit, which is only made necessary by the field being there. Navi shaped as a triangle... that's really just a basic targeting system. OoT invented that kind of targeting system, but other games have made it work without it being a character, so of course OoT could have. I'm ultimately satisfied with it being a character though.
Development team being only three people? There's no way that was ever going to stay that way. That's sounds like a preliminary planning, brainstorming, or prototyping team to me. That's almost not relevant in the game "sucking", to me.
I actually went and read the other articles that this one linked to, as well. Interesting stuff. Them and this provide some pretty cool insight into OoT's design process. Good find Badges! ^^