I think FF:A, which is technically the first title of the Mana series, is better than any 2d Zelda. It oozes soul and has superior lore. Also, the ending also makes me teary eyed.
I think the main thing to keep in mind is always have a lot of keys and Mattocks before dungeons.
It also has cryptic puzzles like AlttP. I beat the game at 9-10 years old without a guide, but I had to use one a little bit at 32.
I consider it better than other Mana games.