I've played both quests several times, but I liked the first quest better. The second quest was a great invention, as was putting two quests in one game in ALttP. How awesome it would be for MM to have a second quest?.
Great difficulty in the second quest of LoZ, better use of the flute and the secondary stuff.... Having one secret in every screen of the overworld map finally fits. Awesome! I tried a lot in the first quest to activate the shop (wasn't it?) hidden in the death mountains of the second quest, I didn't think you had to beat the game completely to unlock new secrets. All you had to do was to use the flute in that screen in the second quest.
The first quest was better balanced though (even if palace #6 should have been the last one).
The sixth dungeon was the hardest dungeon ever to appear in any Zelda game, at least in my opinion. Maybe I was too young back then, I replayed it later and if was reasonable, just like TAoL. The later games are way easier though.
Have you ever seen Wizzrobes, Like Likes AND Bubbles (? - the things that curse you, so you can't use your sword) crammed together in one small room full of obstacles in Ocarina of Time?
Do you remember the Bubbles coming in two colors in the second quest the blue and the red ones?
Do you remember walking more than three screens away, the enemies would return?
Do you remember being under attack, no sword to use, walking back through several rooms with closed doors packed with Blue Darknuts and other tough enemies, no bombs to spare, arrows costing rupees running out....
...Getting a boomerang, no bow, then a flute, another boomerang... The second quest doesn't really loot very well. I like entering dungeons, getting the treasure, kill the boss with that same item and then rip the overworld with it.