I have been slowly going through the game. I played it on the N64 but didn't get real far (can't even remember how far I got).
I got to the Temple of Time last week and just finished the first boss after that (Phantom Gannon). Phantom Gannon was the worst boss (concept not difficulty) so far imo.
The temples/shrines are incredible puzzles, especially considering when they were made. The difficulty progression is just right so far. I have used zero hints (unless you count Navi's talking) and have not looked up anything online for it, so I feel pretty accomplished after figuring out the dungeons and bosses.
Every dungeon I get to a point where I'm on the verge of wanting to give up and then the light bulb hits me and I solve whatever was holding me back. It's like the game is in my head knowing when I'm about to cave and then it lets me in 
I love the 3D, interface, graphics, puzzles, and items. The main song that plays in the plains sounds very Suikoden-ish though...which is great, but it's too close imo...fantastic song but...
I have not done many side quests yet. Gotten one Poe, got all the rupees in the water world, working on shooting all the rupees for target practice. Someone else mentioned that they didn't feel the desire to explore and that's been my feeling as well. In rpgs like Final Fantasy, exploration is one of my favorite aspects (in Mass Effect 2, my most hated part was not being able to explore even as much as the first one...among other complaints)...so I'm a bit disappointed with the exploration aspect of OOT so far. I could look around for side quest stuff...and I would IF it added to the story and/or had new creatures/weapons to find and defeat (ie: Final Fantasy). I know zelda's are not made the same...just an aspect that I've been personally disappointed in.
Not sure if I'll decide to hit those side quest or wait until I potentially do the Master Quest (if I do)
The only other complaint I have is starting back in my house or the beginning of a temple...I want to save exactly where I am at (suppose you can if you just close the 3DS, but you can't access other games/apps)...
I am afraid the difficulty will continue to increase and length of the dungeons will become unbearable for my taste, but hopefully not.
I have truly enjoyed it so far.

Maybe someday I'll be motivated enough to complete the game.