I played Oracles of Ages for the first time last year...Man, the puzzle difficulty was brutal. Not just in the dungeons (which did fuck me up), but also just getting to the dungeons themselves is tough. In particular, I remember having trouble with the Ancient Tomb and Jabu-Jabu's Belly dungeon. I got really stuck on Crescent Island as well. Oracle of Seasons wasn't as hard but still packed a punch.
As a pair, I think Oracle of Ages/Seasons are the toughest Zelda games, IMO. Super complex dungeons, seemingly obtuse puzzles in the overworld, lack of direction, etc.
Because you can only having two items equipped at any given time, Oracle of Ages/Seasons would REALLY benefit from a remake. This is a huge problem in both games, as the puzzles are very complex and require the constant switching of items -- more so than the other 2D games like Link's Awakening or A Link to the Past.