1. Not to that extreme. You literally do the exact same things in the exact same order. 

2-4. With a game that was meant as a sequel to another game, I think there is a point in doing so. There haven't been contradictions to this extent in the Zelda Universe before. 

5. Like I said, it doesn't bother me as much, but it just reminded me of Phantom Hourglass....and I shiver at the thought.

It's still convoluted and unnecessary, each installation of the zelda franchise stands on its own legs just fine and any connection with previous games is so tenuous as to go unnoticed by all but the most crazed and diligent of fans.  And I may have missed it, but when was the last time a man named Julius Caesar marched an army into Rome, took over the Senate only to be betrayed by an old friend name Brutus and his brother-in-law Cassius?  Because I am pretty sure that's only happened once, whereas Hyrule's history is doomed to see Ganon plot to take the power of the triforce for himself from a princess named zelda and a plucky mute fairy guy in a green hat and tunic for the rest of eternity.

This is partly why I am so fond of Majora's Mask and Link's Awakening, because at least they are different.

I thought ALBW is not a direct squeal to ALttP. So, the story is not suppose to be a continuation.

Link has been playing with his Master Sword for quite sometime.

Ganon's only really after the triforce in three games. The first one, where he takes the triforce of power from Zelda, Ocarina of Time; where he gains access to the realm; and Wind Waker; which is the same Ganondorf from Ocarina of Time, trying to fulfill his original plan.

But in the Wind Waker, you see his original motives for getting the triforce. He only wanted what was best for his people. 

And only the Hero of time is ever a fairy guy. 

It's the Legend of Zelda. Each entry isn't a completely infallible historical narrative that should be taken as fact when you play another game. To an extent, they're retelling of the same basic stories from era to era, both in the meta-fictional sense of being the same legend altered and added to within Hyrule, and within the sense that as new generations of players come across Zelda, it's a remix or alteration of the basic elements that have combined to create other games. If you attempt to pick apart Zelda's narrative so that it falls exactly into line with other games, then you will be disappointed. There are inconsistencies because narrative unity is a secondary concern, behind the primary concern of delivering the best mechanics, structure and gameplay experience. That's why I view them as literal legends, which aren't fixed narratives, but narratives subject to reinterpretation that feature the same broad conflicts, themes and structures. Kind of like Tolkien's legendarium, or the Icelandic sagas. To me, The Legend of Zelda is modern heroic-epic, featuring relatable archetypes in the eternal battle between good and evil. Skyward Sword established this with Demise threatening to return time and time again, the way in Tolkien, evil takes shape and returns time and time again, whether in visible, powerful forms like Morgoth or Sauron, or in forms like seflishness, jealousy etc within an individual, which leads to acts of evil. Some stories will be very similar--Ocarina of Time/Twilight Princess, A Link to the Past/A Link Between Worlds--while others will vary. Link's Awakening and Majora's Mask are very unusual Zelda games, but they still feature the fated hero and the incarnation of evil that must be defeated.

And, like Rol, I think A Link Between Worlds could be the best thing to happen to Zelda for some time. If the next iterations take a non-linear approach that avoids hand-holding and rewards exploration and curiosity, then Zelda will be in the right place. Being honest, I think if you play Zelda expecting the story to make sense or the dots to connect extremely well from one game to another, you're missing the point. It's the Legend of Zelda, not the History of Zelda.

Your mistake (as I'm sure others have probably pointed out) is that you're looking for a consistent story in a franchise that thinks that story is an afterthought. Maybe we should demand more but I'm personally happy with what little scraps we get lately.

You really shouldn't read too deeply into the cobbled together Zelda timelines or story.

This doesn't make any sense. It's a video game. Play it, and enjoy/don't enjoy it.

Then why is this the first time I've been disappointed?