The ALBW "cut scenes", if you want to call them that, were very few and far between. IIRC, there were maybe 3 or 4, they occurred only at very important points, they were fast, and they looked visually similar to the actual game play. I'm OK with that.
I'll agree that they were pretty quick, but them looking like the actual game doesn't really mean much sense ALBW, like every other Zelda game, has in-game cutscenes.
And to be frankly honest, I felt like the cutscenes and story telling were sub par in ALBW, and I'd rather they went with the WW, TP, or SS approach to story telling with Zelda U.
Aonuma said in the E3 reveal that he wants the game to be more like the original Zelda. I interpret that as less "telling you a story", and more "you experience your own story". No one is saying that the game shouldn't have story, just that it should be more nonsequential and driven by game play, instead of passive cut scenes. The problem with cut scenes is that, in most cases, games that have them have to be more linear b/c the cut scenes need to be viewed in a certain order. That's why I'm saying to get rid of them and let us tell our own story. I don't want the game to stop me from visiting the snowy mountain b/c i haven't seen some dumb cut scene where they spend 15 minutes explaining the lore of the snowy mountain. Just let me go and explore!
I actually don't think what Aonuma said in regards to Zelda 1 at E3 had anything to do with anything other than overworld. Plus given their stance with story telling, and the fact that while it's incredibly held back and mostly hidden in the manual, Zelda 1 has a story, I don't think Zelda U will be anything like Zelda 1 in regards to story telling, or at least I hope it wont. I can understand wanting to explore, but exploration without a goal is only fun for so long before it becomes absolutely boring and tedious, at least in my opinion. So for me, I'd rather have a linear game that tells me about the story of the mountain, then let's me go explore, and not a game that doesn't tell me anything and I end up on a mountain that isn't significant or in other words not worth exploring. Also, on the note of linearity comming from story telling, to be honest I don't really care if I can explore areas at my leaisure or not, and story telling is far more important than the ability to do any dungeon in any order, so yeah.
To sum up, I don't think Aonuma was talking about story telling at all at E3, and I'd rather be told a story than make my own, as I easily find myself bored in games with little story presence.