It was a super confusing departure from the norm, that's for sure. And with Skyward Sword opting to do the exact same thing, you have to wonder exact what's going through the developer's minds. But you also have to keep in mind that a whopping 100% of modern Zelda games - Twilight Princess, Phantom Hourglass, Spirit Tacks, and Skyward Sword - all lack it as well, so this is slowly becoming the new standard. I do have a few theories concerning why it's been omitted, but keep in mind that I can't prove any of these, and that I have little to no facts to support them.
First off, the most obvious reason would seem to be what someone already outlined above; it was either planned at one time and scrapped, or there just hasn't been enough time to worry with it. From what I remember, Twilight Princess was under a LOT of pressure to be released, so that makes sense, just because it was announced too early and probably got over-hyped. But.... that's kind of where the reasoning ends for me. Phantom Hourglass and Spirit Tracks really don't seem like they would've taken a massive amount of time to create when you compare them to TP and SS. And on top of that, was there ever ANY pressure to really release those games? I mean, it's not like the entire world was pumped for them, and honestly, on an unrelated note, I consider both of those to be bottom-of-the-barrel Zelda games. Adding that to the fact that they were both direct sequels to Wind Waker, which sported the magic bar, I can't really justify them not having it. Skyward Sword is kind of the same..... But I guess you could argue that SO MUCH MORE was going on with that game. You had the new graphic style, the new level-based style of progression, and of course the completely revamped combat scheme. Combine all of that with all of the new things SS did, and I could understand why a magic bar was the last thing on anyone's mind. (I really don't get PH and ST lacking it though...... Maybe because no other handheld game ever had one?)
My second theory is that...... Maybe magic was getting kind of obsolete and boring anyway. I can only speak for myself personally when it comes to this, but I found that in the three 3D games that had one, (Ocarina of Time, Majora's Mask, and Wind Waker) I never depended on it that much. This is especially true for OoT and MM, where I would purposely omit elemental arrows and the goddess abilities just because they were never super necessary, and I guess I'm just a resource hog like that anyway. And yes, I know about the light arrows. But is having just those alone really worth the magic bar? I don't know really, because it varies so much. I will admit though, the Giant's Mask/Chateau Romani was a nice little quirk in MM.
I also feel that WW does the same thing for the most part. The major exception to this is, of course, the Deku Leaf. Because that thing could completely break the game without a magic meter to keep it in check. So I think if more items like that were invented, a magic meter would hold some relevancy.
All in all, I think we can learn to live without it. Sure, having more things to use at our disposal is always fun, but don't forget to think about why the magic meter was there in first place, and how it could get rather stale as a gameplay element if new things weren't built around it. That's probably the key to all of this; developers haven't found a way to use it in a new way that isn't repetitive, so they took it out. Zelda has always been about gameplay innovation anyway.