Not sure where you are getting this from exactly. Twilight Princess is the best selling Zelda game (if you count both GameCube and Wii, and if you just count the Wii version, then it's the second best selling Zelda behind Ocarina of Time which he also worked on). Anyways, I love Aonuma's Zelda games personally with Ocarina of Time and Twilight Princess being my two favorites.
I do not agree with all of these opinions and am simply arranging everything I've ever heard/seen that was critical of modern Zelda.
"Serious Fantasy action-adventure with creative, unique dungeons and an overworld" seems to be what people want out of the series. I say this based on how the first LoZ, Zelda 2, OoT, and TP are the best sellers.
MM sold less because it was explicitly depicted as a side story- "Zelda Side Story" was literally its Japanese title. The game's fans often cite the unique plot and array of side characters as an awesome thing, but if a person is merely looking for a plot that works as background, then they would have probably been put off by that. Many gamers also seem to have been stressed out by the time limit and the resulting weird game structure. It was also released absurdly late in the system's life.
Wind Waker flopped relative to expectations because the idea of cartoon Zelda clashed with the idea of dangerous, serious fantasy adventure in the minds of a large number of people, and that was how people defined Zelda. Maybe it wasn't an accurate reflection of how the old games existed in the minds of the creators and something was lost in translation via the low-quality graphics, but that serious depiction of the game is still what formed in the minds of most kids that grew up playing OoT. They'd best cater to this fanbase for two reasons: 1, Quite a few known customers already exist, and 2, other games like WW that deviate from those standards had the chance to bring fans to the series and failed.
Between people who hated sailing/the Ocean, the triforce quest, and (the smaller group of) people disappointed in the dungeons, the game also lacked the positive word of mouth to overwhelm the bad first impression.
The "purple lunchbox" negative reputation of the system probably made things worse for the game but this reaction would have happened on any piece of hardware.
The DS games are generally the least popular in the franchise beside the CD-I stuff. Commonly cited complaints are:
They returned to the WW art style, which was a misguided attempt to make up for the ds' hardware power, for the system couldn't even make cel-shading look good.
the touch controls decreasing direct control over Link, making the base combat less satisfying.
The train and boat were poor substitutes for an actual overworld.
The dungeons revolved almost entirely around puzzles, which were also brain-dead easy more often than not (though the boss fights, in my opinion, rocked).
TP happened as a direct response to Wind Waker's reception. "People rejected whimsical Zelda? Let's make a more serious one." The best-selling Zelda ever happened because they looked at a game that Aonuma designed and attempted to do the exact opposite. This in particular makes it easy to think that his ideas have decreased Zelda's popularity.
I am not qualified to talk about SS firsthand. I did not make it very far past the tutorial yet. Things I have heard: Mainly that the motion controls wound up wasted on excessively puzzle-like battles. Some people didn't like whatever was done with the overworld structure. The two non-internet people I know who played it actually really liked the game.
A lot of people speak harshly of the combat vs puzzle balance in the franchise, and say that puzzle content should be dialed back in favor of more battling. When I played LoZ for the first time, I was surprised by how resoundingly familiar it felt to me despite the near-absence of plot and puzzle elements which have had large presences in all the Zeldas actually released during my lifetime. It's made the large majority of Modern Zelda's puzzle elements feel like filler to me by comparison. I do think that they are holding the franchise back from being the industry-defining game franchise it once was. A smaller number of really cool puzzles would make for better games overall.
As for misc criticism, maybe people blame the guy for TP and SS's horrible tutorial segments?
Also, Miyamoto definitely had the majority of creative control on OoT and counting it as one of Aonuma's creations is not accurate.
edit: Dang that turned out longer than I expected.