The 2D games are certainly tougher. Perhaps the top-down view plays a part...for example no Z-targetting of enemies, you just have to aim your swings and bows properly. Granted the 2D titles wouldn't require it in the same way that 3D titles would, but it still makes a difference in how easily you can accurately hit enemies.
I really don't think this is the main difference however. I think a lot of the difficulty is accredited to other things:
#1) Enemy damage is a lot higher. In ALttP overworld enemies will knock out a full heart of health if they hit you twice. It's a lot easier to die if you aren't careful. In 3D titles, for the most part you can be as careless as you want as you run around and you probably won't die. The cave in Faron Woods in TP for example, infested with keese and Deku Babas, I've ran through it before without taking care to avoid hitting any enemies as I run past, and I think the most health I lost after I came out of it was perhaps 3/4 of a heart. You couldn't get away with running around with such carelessness in ALttP without being punished.
#2) Less heart containers! Less to collect means they're scarcer and harder to find. Additionally, the maximum you can receive is usually
14 hearts or so,
not a whopping 20. When having less health is coupled with higher damage dealt by enemies, it makes for more threatening difficulty, especially in dungeons.
#3) Less
bottles, or so I believe. I've been playing through OoS and though I'm nearing the end, I'm still yet to see even a
single empty bottle. Fairies for back up become a no-go with that, and couple that with more enduring bosses, it becomes tough. And while there is potion/medicine, it has more restrictions to get. in NES LoZ, only the
first time you buy red medicine for a dungeon do you get to use it
twice. Use it once and it will turn into blue medicine that you can use once more in that dungeon...unless you die after using it! If you go back to re-buy it a second time for the same dungeon, it will allow you to use it twice no longer...once you use it, instead of becoming blue medicine that can be used again, it will revert to being the letter you gave the old lady originally to be allowed to buy medicine. Basically, what this means is that you have only "one shot" to get through the dungeon with two helpings of medicine. If you screw it up, you'll be allowed no more than
one helping of medicine for every subsequent attempt after that! The pressure is
ON! It would sound like not too difficult a deal to get through a dungeon with two helpings of medicine on your first try but.....I remember the 6th and 8th dungeons (Dragon and Lion) in LoZ gave me a LOT of trouble. Those rooms with the Darknuts and Wizzrobes and Like-Likes all clustered together....and those rooms with eight or so red and blue darknuts....ugghhh tough times.
#4) As I mentioned above, the bosses are more
enduring. They are not as easy to defeat, and it takes a longer amount of time to do so. Additionally, often times their blows are more difficult to avoid than they are in 3D Zelda. Add that ontop of the above mentioned factors, and it makes for a legitimately tougher fight. You really have to figure out how to master your technique for avoiding taking damage while effectively dealing it (don't even get me
started on
Moldorm ) because let me tell you something, you are
not going to get through the fight by sword spamming and fluking as you might perhaps get away with sometimes in 3D Zelda. And while it's not uncommon to defeat 3D bosses on your first try, with 2-D bosses, you really have to
work your way up to defeating them, trying again and again until you perfect your technique and master the battle. 3D Zelda often times really doesn't require you to build up the same level of
mastery in order to pass it.
#5) Save points in dungeons. In 3D Zelda, for the most part if you die, it's not all that difficult to get back to the point you were at, even with respawned enemies. But 2D Zelda features tougher rooms to manage getting past without losing a lot of health; having to repass those rooms again becomes a problem (I present to you the rooms with eight darknuts in them in original LoZ)
especially on the way to a boss! Sometimes you die before you can even make it to the boss door! Forget stocking up on health for the boss battle, by the time you get there, you might only have half a heart of health left! In 3D Zelda, boss rooms usually have easy access; for example in
The Wind Waker, you have the Warp Pots that will take you
directly to the door. In
Ocarina of Time, the boss doors are usually set up to be in places that you can immediately reach upon entering the dungeon, as in the Forest Temple, the Fire Temple, the Water Temple, etc. And lets not forget, usually 3D Zelda bosses have a plentiful item restock in front of the door, including fairies, to assure that you are at full health...not so with 2D Zelda. In fact, I may as well mention you have less stock of everything to begin with...less bombs, less arrows...you're definitely not allowed 100 bombs or arrows on you, that's for sure (although this is disputable with arrow-rupee tradeoff, but even then you have to watch how many rupees you are willing to use on arrows...)
I should also mention that I hear this is particularly bad in AoL, as every time you die in the overworld, you end up back in the original room at the start where Zelda is sleeping. You might not even
make it to the dungeon in the first place! :S
So certainly, 2D games have tended to be harder.
However, these factors are not particularly
unique to 2D titles! What I mean is that if they wanted to, Nintendo could take these factors and apply them to 3D Zelda as well; it just so coincided that when the series evolved into 3D, these difficulty factors were forsaken for easier accessibility. If Nintendo changed their mind, I believe it would certainly be possible for them to implement these factors in a 3D Zelda title as well.
We'll see how Skyward Sword fairs when it comes out.