"And I've heard complaints about, say, Secret of Mana, when your team members would become stuck behind trees."

I don't think that's really the same thing. For one thing, you're not going to fail any missions, even if your extra party members die. You just have to revive them like you would in a normal RPG. Only if all three of you die is it a game over.

Ogre Battle 64 had some "protect" missions, but I think that even if you fail some of them, the game continues, but will branch off on a different story path. Others, I think if you fail, you do get a game over, but I can't really remember because I haven't played in so long.
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