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Navi (which might not be her final name) has some significant advantages over signs alone. First of all, she's more intelligent. She won't speak up until you've been staring at a puzzle for a while. If you figure it out right away, she won't pester you. And if you're still stuck after the first hint, she can offer more help. She can also comment on signs you read, the items you've found, and anything else that might be relevant.
It's also easier for me to write hints this way, because Navi's also trying to figure the puzzles out herself. With signs alone, there's often no clearly optimal thing to write. They have to be deliberately obtuse to avoid spelling things out, but, of course, some players will need more help than others. It's hard to find the right balance. Navi, on the other hand, can more naturally hint at how the solutions work as she thinks them through, starting with subtle prods and making things plainer as needed.
If that all sounds terrible and the quest is ruined forever, don't fret: Navi's disabled by default. If you don't tell the game you want help, you'll never know she's there.
