4) Combat is way too easy - This is something that has slowly crept in over the years. The original's combat was challenging and intense, and The Adventure of Link had sections that were harder than Goron turds. But as time wore on, the battles became increasingly less challenging. This wouldn't be so bad except that the puzzles have remained fairly devious, causing an odd disconnect. For me the worst was in Wind Waker, which had a couple of puzzles that stumped me for hours, yet common enemies and even most boss fights provided little challenge.
If you disagree, that's fine, but the optimal solution would be to finally institute a difficulty system of some sort. But as previously mentioned, Zelda designers are lazy. Besides, if the combat were too hard, it could completely halt a player's progress and ruin their experience, whereas if it's too easy, the worst that can happen is that they'll futily rant about it on the internet.
3) Heart pieces don't matter - One great thing about Zelda games is that there are tons of secrets hidden everywhere. In Majora's Mask, many of these secrets were masks, some of which actually granted you new abilities (like the "bomb mask" that let you explode your face). However most of these secrets are "heart pieces." Collect four of these, and get an extra heart added to your life bar. Which is all well and good except that every time you complete a dungeon you are granted a "heart container" which immediately increases your life total by a heart, rendering the number of heart pieces you've collected pretty insignificant.
Let's say after 4 dungeons you've found 10 heart pieces. Sounds pretty impressive, except that when you add the 4 heart containers you got automatically to the 3 you started the game with, the extra 2 you got from all that secret hunting aren't exactly game-changing. Of course if you rewarded skilled player's too much, the combat would become more of a breeze to them than it already is. And the easy combat is another reason why heart pieces don't really matter.
2) Rupees really don't matter - With rare exceptions, you will generally have a full purse. This is because rupees fall out of every enemy, pot and shrub. But it doesn't matter because there is nothing to buy with them, aside from bombs and arrows which fall out of every enemy, pot and shrub. On the rare occasion that you actually need rupees for something quest-specific, it usually costs more than you can hold, meaning that you need to obtain the "bigger purse" mcguffin in order to proceed, rather than actually being faced with a decision about whether you can afford the item, or at least how to go about raising money. Not taking the time to balance an actual money economy is ***drumroll*** lazy.
1) It's Ganon! ...again - Spoiler: the big-bad is nearly always Ganon. This wouldn't be a big deal in and of itself, except that the games always try to spring it on us as a surprise. At this point I would be much more surprised if the twist in Skyward Sword is that it's not Ganon. o.0
But despite these niggling flaws, if you say anything bad about Zelda games in my presence, you will be Gannon-Banned.