I see what you mean, but you're inaccurate.
The villain Link meets at the beginning of the game gets hijacked later on. Zant and Ghirahim are a lot alike, in that they are each trying to free their imprisoned master and both are a bit "unstable".
Ghirahim wasn't carelessly thrown away like Zant was, though. He was actually important to his master's revival. If it weren't for Ghirahim, Demise would never have returned. He was also "unstable" the entire time. Zant had his character ruined by becoming that way, as he was calm and effortless beforehand. To add to that, Demise had a presence throughout the entire game, unlike Ganondorf in TP.
The games were both far too linear, and there were a lot of barricades to exploration.
Skyward Sword's
story was linear, yes, but the gracious amount of side-content allowed for open exploration throughout the entire second half of the game, which is one thing TP failed at. In all honesty, though, he whole "linearity" thing doesn't really matter. It's about if the game is good or not, not if it's linear or non-linear. That's really one of the silliest arguments in Zelda (and gaming) imo.
The Silent Realm is like the Twilight Realm, and the set-up of dungeons is similar.
The Silent Realms are absolutely nothing like the Twilight Realm save in eeriness. Of course, unless you mean the Twilight that blanketed Hyrule. If that's the case, then yes, but they weren't boring and tedious. They were thrilling and enjoyable to go through.
The first three dungeons are spent trying to find something; in Skyward Sword's case it's Zelda, and in Twilight Princess's case it was the fused shadows.
Looking for Zelda and collecting three items aren't comparable by any means. Searching for a friend provides a legitimate drive to keep going in the game. It was about wanting to catch up to her rather than just finding something to defeat the evil of the game. In addition to that, the second half of the game wasn't a copypasta of the first half of the game, unlike TP, and it added an extra element to the game instead of taking one away (the Silent Realms). Now, if the whole first half of the game was about finding those tablets to unlock the next area (which would have been quite silly and pointless), that would be a different story. But that wasn't the case, so it doesn't matter.
[T]he next string of three dungeons is spent trying find something else in order to gain access to a new area. In Skyward Sword it was where Zelda is, and in Twilight Princess it's where Zant is. In Skyward Sword it was where Zelda is, and in Twilight Princess it's where Zant is.
Searching for the three flames was just having to take the long way around to find Zelda. The whole point of the game up until Zelda was found was aimed at finding her. The forging of the Master Sword just came along with it. It wasn't like TP, which had a major plot twist and an obvious second half to the game. SS's transition into the second half of the game was seamless, and it didn't have a major twist in the plot. The major twist was saved for when Link found Zelda, which is about 85% into the game. That's quite a bit different from what TP did.
And the final boss in both games can be distracted by an item for an easy win. In Twilight Princess, it's the fishing rod and in Skyward Sword it's the bug net.
Demise's fight felt nothing like Ganondorf's fight. One, the buildup to it was constructed throughout the entire game, unlike in TP where the buildup to Ganondorf was basically right before he was fought. Two, Demise was the final part of the final sequence of battles, whereas it was Ganondorf the entire time in TP. The Fishing Rod and Bug Net things are also just easter eggs. They're not designed to make the fight easier, and it's actually quite difficult to use them properly to gain an advantage.
There's a sidequest where Link has to collect a large quantity of a specific items in order to change someone into a human in both games.
That's not a legitimate point at all. And the whole "turning someone to human" thing has been around since OoT, so it's not like TP was the first to do it and SS stole it from TP.
All that said, I guess in some ways SS is a TP 2.0, but in many other ways, it's a redemption status of where they failed in TP and a way of saying, "We did these things wrong before, but we're showing we can do them right," which gives them major respect (and, in some ways, style) points. If it were a TP 2.0, it would have failed everywhere TP did. But it didn't. That's why it's not a copy/paste of TP. It took all the good aspects of all the games in the series and blended them together to flow with each other in harmony, as well as added a few new things to the series (dashing, true motion controls, stamina gauge, etc.), which shows that they weren't taking things only from TP and recycling them. I respect opinion, but you couldn't be any farther from the truth by calling SS what you have.