Try Lufia 2, if my memories are correct it had terrific puzzles. The game had same-turn movement as in roguelikes and that was the base for many timing puzzles.
Ahh, Lufia. I only played Ruins of Lore (the 4th and last spin off game in the series, not counting the remake I think they did) back in the day, which I thought was pretty great. Been meaning to play the other ones for ages. I don't remember a lot about the puzzles, I need to get my gba out and replay that sucker
Back on topic, I heard Sven saying in the latest update that they'd fill the dungeon with a variety of things, including puzzles.
