For me it's the score (very weak, in my opinion. Always the same boring little theme playing), the animation (it's not that awful, per se but what really bugs me is the difference between the original characters in TLK and in SP
This:

looks nothing like this:

and how their personalities were handled in this movie.
I'm not too crazy about the songs but "He Lives In You", "Love Will Find a Way" and "One of Us" are very good, especially "He Lives In You".
"My Lullaby" could be better, the whole "Upendi" scene is AWFUL and "We Are One" could be good if the male singer had a stronger voice.
The story has plot holes and incoherencies but they did what they could do to make this story fit with the original. They can't touch the original to make SP a better movie.
Of course they had little to work with. Low budget, it was produced by Walt Disney Television Animation (or DisneyToon Studios, it's basically the same animators from tv shows like Timon & Pumbaa), it was animated mostly in Australia (Walt Disney Animation Australia), and it means virtually nothing to Disney.
I'm not trying to bash SP in any way but at Disney it goes in this order:
A - Classics considered to be masterpieces, popular, oscar winning, they sell anything and everything. (TLK, etc)
B - Classics in the true meaning of the word, popular and meaningful to the studio (Lady and the Tramp, etc)
C - Classics considered average (Sword in the Stone, etc)
D - Classics no one really knows (Three Caballeros, etc)
E - Classics that were huge financial flops and embarrassments to the studio (The Black Cauldron, etc)
F - DTV movies made to make easy money from A and B movies (SP, etc)
Producers can have the best ideas but without money and support you can't always make a movie the way you want. They've done the best they could do and it's better than Pocahontas II or Hunchback of Notre Dame II (these two are downright AWFUL, in my opinion).
So yeah, as far as sequels go, SP is an average one for me, not awful but not great (mostly because TLK has some big shoes to fill).