Defintely the low popularity of most sequels is a possibility as to why they are not in the same calibur as the original. Only a few sequels in my opinion have lived up to be better than the original (Terminator 2, Spiderman 2, Godfather 2). It seems like people can get VERY excited for a second movie in a popular franchise, but once a third or fourth movie in the same franchise shows its face, people decide that the franchise is worn out and has lost its magic. That's most likely why the LBT sequels are met with such poor remarks, because none of them will ever be able to capture the magic, or dark emotion, the first two or three movies made.
I also believe change in actors also creates problems. For example, most noticeably LBT, the change in voice actors for Littlefoot and Ducky probably did not bode well in the long run, but then again the kids who watched LBT II were probably not old enough to remember the voice actors of LBT I. In most cases, a change in actors usually leads to this constant complaining, "He'll never be as good as the original guy," or "She doesn't fit the role like the first girl." That was my main problem with Mortal Kombat Annihilation, because Bridget Wilson and Christopher Lambert were both terrific in their respective roles as Sonya Blade and Raiden, but changing them in Annihilation was a bad move. Sometimes the writers can't control this because of extenuating circumstances, like in Harry Potter where the actor who played Dumbledore in the first two movies died so they were forced to find a new actor.
I think writers are sometimes blinded by the success of certain sequels that it clouds their judgement in these situations. The Godfather II was an AMAZING sequel, so much better than the original in my opinion, and the same applies with Terminator Judgement Day. I feel writers look at successes like these and try too hard to match their quality that they don't stop and think about what exactly they are doing.
Most of all, I think in Disney's case, the sequels are made entirely for this generation instead of the former generation of people who saw the original movies. For example, I watched both Bambi II and Fox and the Hound II recently. Both of them were good movies, but terrible sequels. I think Disney is really trying to win the kids of this generation that they really don'y pay attention to the older generations who loved the originals.