I will admit the Oracles games have better dungeons and are more challenging overall. There's a part in Seasons where you have to change the seasons in a specific order to open access to some area; that stumped me as a kid. Whereas the only thing that kinda stumped me with LA was the final boss sequence.
That being said LA is still the best to me. Will I sound like too much of a cigarillo if I admit I loved the story? The music is amazing, I loved the characters, etc; I've beaten it more than any other game. The Oracles are amazing as well, but perhaps the nostalgia factor is too powerful with me and LA.
LTTP on the other hand...meh. I still haven't beat it and it's been collecting dust (with my DS) for months. I've never played Minnish Cap. PH is interesting. The control mechanics are very fluid, the graphic style fits the DS well, sailing is improved over WW...but after a couple weeks I put it down and never picked it up again. It just didn't capture my attention