Well, this question is truly based on opinion.
Dark Link - I will admit - was a bit tougher for me than Morpha ever was. The fact that he could mimic your every move and hop on your blade and attack you like that was definitely an unnerving experience. Morpha was an overall easy boss, you just needed to get a rhythm down on when it was dangerous and when its weak spot would reveal itself.
And in actuality, you also have to think of the dungeons. It wouldn't make sense for him to be the boss of the Water Temple, merely because he's a not a water-based enemy. Morpha, however, was. I feel he could have worked better in the Shadow Temple, because they repeated Dead Hand as a mini-boss when it was a boss in Beneath the Well. I feel that Bongo Bongo could have been the mini-boss and Dark Link be the overall dungeon boss, but like I said earlier, it's all opinion-based.
My opinion is that he really shouldn't have been. Ignoring the placement of him - and a good area where he could have been placed - we have to glance at it from a difficulty point of view. Many people managed to "cheat" against Dark Link, whether it was simply using Din's Fire or using the Biggoron sword. Not to mention he was a much easier battle if you were doing a three-heart run, considering the fact that he shares your amount of health. So really, I don't think he should be a boss, simply because although he had potential, he just wasn't at a boss-difficulty level.