The series Golden Sun is my favorite for dungeons and puzzles, gotta say. On the topic of skipping puzzles, I think the latest game in that series had an ability that showed you the solution if you are too lazy.
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.
Use a fast-forward enabled emulator because as most jRPGs, blabber blabber blabber fedex to this town and find the dungeon, down the boss, continue story.
EDIT:
All monsters appear on the dungeon map as well, and can be avoided if the player wishes. Motion in dungeons is also "turn-based," in that monsters do not move unless the player does. Maxim gains a number of tools and weapons for use in dungeons (similar to the The Legend of Zelda titles), such as a bow and arrow, bombs and a hookshot; these, along with his sword (swung using a face button), will stun monsters temporarily and interact with obstacles. Finally, dungeons place great emphasis on challenging puzzles.
