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I'd say that OoE is clearly the most difficult CV on GBA/DS/3DS.
Depends on how you look at it. The games had very different ways of scaling their difficulties.
To make a long story short: CoTM ditched the shop functionality, reintroduced a rigid, bare-bones whip system, multiplied uncomfortable environments, and aspired to be as user-hostile as possible. Unsurprisingly, it was hard.
OoE skyrocketed item prices, topped enemy health and power, made bosses incredibly deadly and resilient, and focused on pattern recognition and weaknesses. After the supreme battling ease of the Sorrow games, OoE came off as 'shockingly' difficult to its contemporaries (
I was relieved).
So it probably isn't as "clear" as you'd expect.
Now, as for which game
best handled its difficulty, that's essentially a matter of personal taste.