Here is my list of sequels that are better than the original, in no particular order. For the sake of the list, only one sequel per main franchise.
Avengers: Endgame

Endgame has everything, high stakes, a huge cast, a strong plot and it was bold. Avengers: Endgame is currently the longest Marvel movie clocking in a little over three hours. It is both the biggest and most intimate Marvel movie yet. For the purpose of this list, Avengers: Endgame counts for the Avengers movies. Other sequels that make the list would be for their respective franchise.
X2: X-Men United

X-Men 2 is still one of the best sequels of the X-Men franchise. It is action packed and has a great ensemble.
Puss in Boots: The Last Wish

Out of the Puss in Boots movies, The Last Wish far exceeds Puss in Boots. Is a great movie with a great story and it is hilarious.
Shrek 2

Out of the Shrek films, Shrek 2 still ranks as the best. Shrek 2 also gave us Puss in Boots who has become a fan favorite character.
Spider-Man: No Way Home

Easily the best MCU Spider-Man movie, it tops both Spider-Man: Homecoming and Spider-Man: Far From Home and it successfully unites Tobey Maguire and Andrew Garfield’s respective Spider-Man movies.
The Dark Knight Rises

Christopher Nolan has the best Batman trilogy yet. We have to wait and see how Matt Reeves does with the next two Batman movies. For me The Dark Knight Rises is the best out of the trilogy. It is bigger, longer, and a satisfying conclusion to the trilogy.
The Lord of the Rings: The Return of the King

Epic. Emotional. A satisfying conclusion to The Lord of the Rings trilogy. It deserves every Oscar it won back in 2004. It won all eleven categories it was nominated for.