Hm, this is a really good question and I'm annoyed by the fact that I didn't get to it sooner. I'm not going to pick the best hidden out of every generation because there should only be one absolute Legendary Pokemon that was best hidden. After thinking about it, for me, it was most definitely Lugia, mostly because when I was searching for Lugia, I was about seven years old, I didn't possess a walkthrough and I didn't even know that Lugia was in the Whirl Islands. However, I decided that I wanted to search the entire Whirl Islands because they surely existed for a reason greater than the player being able to obtain a few items and catch a few Pokemon. I remember stubling upon Lugia by accident, but before I even started the battle, I knew it was Lugia. After watching the second Pokémon movie, I had more or less pieced it together during my three day search in the Whirl Islands.
The Regis would've been amazingly hard if I hadn't had a walkthrough to know where they were, but they were quite easy to capture with a step by step guide, even if it took the fun out of the game just a tad.