Hm, never seen it getting hated much. Then again, I don't see LA mentioned that much either, but I did know it has sort of a black sheep image. Personally, what I think could throw some people off is the inclusion of tons of Mario stuff in it. Not only the sidescrolling, but... well, learning ocarina songs from a Wart expy and fighting goombas in underground dungeons along with the copycat shy-guys did come off as a little unexpected. I mean, I know when the game was made it probably didn't look that out of place and the whole dream thing rationalize it well enough, but as someone who played it recently without knowing much about it beforehand (other than it being Zelda) and having grown up with the newer games on top of it, it did look... well, you know how, at first.
...but even then, that doesn't warrant hatred or being considered a serious inherent flaw. Not that I see at least. Closest thing I'd call to a flaw is the saving system, not for being bad as much as not very straightforward. Might be just me, but the button combination used for saving elluded me for a while... but I guess I brought that one on myself. (I have kind of a preference to use the game's own save system rather than the virtual console's, no matter how impractical the old system is)