I personally hate the Heros that never say anything. Ever. Why? It makes me angry. The most you got out of Isaac in Golden Sun was the "yes" or "no" response, which, in most potentially story changing situations, when inputting the "wrong" answer, you got something like - "You don't mean that!" Try again. Or worse, "You don't mean that!" Another character decides.
Those RPGs that follow the tried, tested and eroded, cliched and boring, "collect the elemental crystal" escapades that takes to to get the fire crystal from the Desert/Volcano, the Earth one from the cave/mountain, plant/earth one from the forest/jungle, water one from the remote island, Lightning one from the metallic structure, Ice one from the Ice cave - which is on the same latitude as the volcano/desert, the wind one from the mountain peak, and so on. It is boring and repetitive, and at least in ToS, it gives you a reason before it gets boring.
I agree with the having to solve the town's calamity before being able to progress, and some of the villains... ugh. Big, fat and hairy, they'd do a better job as Homer Simpson that "taking over the world", leaving every open space for you to win right open.
World Maps. Yes, it's easier, but I hate the way that you can get across the whole world in an instant, ebing so huge. Yes, it's a representation, but I fell like I'm missing out. That's a good thing about Pokemon, I thought.
And, I suppose that's all my qualms for now, until I wake up at 3am and think of something else in a dream.