Back in the day you had games like Secret of Mana that were pretty special for this. But it wasn't perfect. Sometimes a character would get caught on something in the background, which would really suck. Luckily that didn't happen so often.
Team Ico's games come to mind. I don't know if I'd say their super smart, but they're very life-like. Ico, Shadow of the Colossus, and Last Guardian are all really built around the player character interacting with an AI character.
Resident Evil 4 also did a really good job with Ashley. Even though most of the game is an escort mission, you never really run into any of the problems normally associated with that.
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