You are fairly close to being done, but I did personally find the endgame to be longer than I expected (this was a good thing). Though you're not exactly into the endgame until after you've beaten the Sand Temple.
When I first reached the Ocean Realm and saw the inaccessible Pyramid, I was convinced that it was a secret, final dungeon where I would end up facing Ganon. I was happily proved wrong.
I actually loved that Zelda was afraid of rats. Every time I was like, "ugh, she's such a girl," but that's just it. It wasn't, "ugh, she's such a princess," it's that she felt like the kind of girl I've known, and because of that, I felt that I could relate to her well. It really fleshed her out as human. She wasn't this wise, prophetic princess, she was a young teenage girl that happened to be a princess named Zelda.I agree. While every time this occurred in the game, I had the exact same complaints as you guys, looking back on it I completely see the logic gameplay-wise. And sure, Zelda has a sword and big armor, but if you see a spider on the wall, it's not really going to hurt you, is it? Yet many people would kill it. Fears are scarcely logical. She still looks kind of stupid doing it and even seeing the logic I will rage at her doing this, but they had something in mind when they implemented it.
Also, it's hard to complain about Spirit Tracks when you look back to Zelda in past games where she's an obnoxious damsel in distress. I actually found Spirit Tracks Zelda to be pretty likeable, whereas in A Link to the Past she pisses you off right from the get-go by spamming her opening speech until you find her. Because after the fifth time you're still not sure where she's being held captive and what she wants you to do about it.