There's no denying the game is different, but that doesn't make it bad.
I remember when AoL was first released. Personally, I loved LoZ, and I wanted AoL to be just like LoZ... but somehow better and with improved graphics or gameplay or... you know, whatever. What we received was not what I expected, leaving me feeling a little uneasy about the series. In fact, I remember the same feeling after buying Mario 2, but that's a different discussion. Anyway, I find that the level of action the gameplay provides is easily more entertaining than the original (which is technically what I wanted out of the game in the first place). The only issue I had to get past was the fact that it was different.
Is there any disagreement that most of the NES's greatest games are 2D sidescrollers? It's logical that Nintendo would want to put a Zelda game within that context as soon as possible. And, while at the time it did surprise and slightly disappoint me to not get the game that I had imagined, the challenge and overall experience of AoL was more than enough to keep me playing as hard as possible to beat that game... and boy did that take a long while.
On the subject of whether or not Zelda would have gone 3D or whether we should thank AoL for the current state of the Zelda franchise: of course Zelda would have gone 3D. However, I find it important to point out that the early experimentation with the series says just as much about Nintendo as it does about Zelda. Nintendo, like any other entertainment business, wants to reach as much of its fan base as possible. Believe it or not, there were some gamers out there who didn't like the presentation of LoZ but who were more inclined to play AoL because of its use of 2D sidescroll. I'm sure it sold more impulse game buys than the original for how awesome the box screenshots were. <-- Opinion, Hearsay, Etc. Bottom line, now games are expected to be in 3D. And when something trumps that we'll expect games to follow the upgrade. It's fun to think that AoL may have had a hand in the jump to 3D, but you'd have to expect that evolution to occur whether AoL had existed or not. I offer a little thanks to AoL for taking the role of the experiment that didn't work well. Don't get me wrong. I like AoL; it's still entertaining for me to this very day. But I'm well aware of how the rest of the Zelda community felt and still feels about its existence. And as such, I thank AoL as something different and for being the battle scar of the series.