I don't think they have intentionally ignored magic, more along the lines of not being able to find a place for it whilst trying to roll out new gameplay. However, I truly believe we haven't seen the last of the magic bar.
I wish magic made it back into the game. It really added that next level of fantasy into the game which made the games more fun. I liked the spells in OoT, and using the magic bar to control things like the Deku Leaf in Windwaker. Maybe Nintendo could implement the magic bar in a way that isn't mandatory in the next Zelda title, and may just give the player an advantage.
I don't think that the game developers completely trashed magic. Throughout all of the games, whether it's blatant and obvious or subtle and smooth, it's been in the game. Sometimes it's that unnatural things that can be called magic. eg: Bird Statues in SS. They work on nothing! MAGIC! Skyward strike seems like a magical element to me!
Twilight Princess did have a magic bar originally, but it was cut. Want proof? On the back of the case (I only know of it on the Wii version, but check Gamecube anyway) look at the picture of Link fighting the darknut in the Temple of Time. Now look beneath his hearts. There is a distinct green bar, yet the lantern isn't in the quick inventory. Shout-out to Unseen64 for pointing this out!
I really hope that magic returns in the future. Just because the Hylian DNA diminishes over time, doesn't mean that magic should just disappear! Nintendo really missed a great oportunity to re-implement magic into Zelda when they released Skyward Sword. The Fairies could give Link magic, or the Shiekahs could, or Zelda could, or something. Zelda benifits more from having Magic than not having it. Twilight Princess is my favorite game in the series, but I wish Nintendo would have included magic in the game. It would have felt more like a Zelda game that was realistic in nature, than real life pretending to be a Zelda game. Anyways, Zelda is great even without magic, I just feel like it should be due to make a big return!
The Magic Meter has not really been used well except in A Link to the Past. I would love to have a magic meter return, but you couldn't find magic in bushes/jars so you were required to carry green potions around. I never buy potions in Zelda...only capture fairies