IDK, I feel like Link Between Worlds is actually one of the most popular Zelda games. I often have this problem with pokemon games where I think they are not that popular, but it's just that people don't talk so much about their 3DS and the games they have on them, but everyone seems to have one and everyone seems to play pokemon and love LBW.
That said, I don't think the game is flawless by any means, but I do think it's on the list of best zelda games, and very high, mostly because it gets all the most important stuff really well, and recaptures something everyone loves in zelda and that had been needed for quite some time, that is the non-linearity.
A Link Between Worlds was a great adventure, albeit it a little on the short side. The dungeons were easier in comparison to its predecessors, but I thoroughly enjoyed each one of them. I also was fond of the game's gimmick of merging into walls to explore new places. All in all, the game is one of my favorites on the 3DS.
The wall merging mechanic is nothing short of brilliant. When I try to think "main zelda game mechanics" that top or get close to it, I can only think of Majora's Mask time travel mechanic, and it's hard for me to even say which one is better (I would say wall merging in general as it's more integrated in the game and in many smarter ways, but as a single mechanic in and off itself, time traveling in MM). I would even go as far as saying that wall merging has been the best and best implemented game mechanic ever. Period. Though that's just my opinion, and just off the top of my head, I'm subject to changing my mind eventually.