The Matrix is an often used example, but for me it’s the Alien Prequels - especially Alien: Covenant really makes the Original Alien much worse. When the original was released in 1979 it had the perfect Monster. A dangerous killing machine of unknown origin. The missing background of the alien is a big part of its scary mess. It’s a blank space in its mythology that the viewer can fill with many explanations. As these explanations are not precise they don’t have to be logically coherent.
Covenant (and to a lesser degree Prometeus) wanted to fill this blank space and tell us the aliens origin. But once you fill out this missing piece of information it is fixed and can only be one piece. There exists now only one singular explanation. And its a boring: The Xenomorph is basically a creature with it’s origins on earth (because David, who’s origin is on earth created it).
I find this hugely dissapointing. The biggest dangers of deep space are all human in origin is extremely small minded.
(Star Trek: Beyond had the same boring plot - the mysterious villain turned out to be a human after all. As if only humans are capable to pose (or create) a serious thread to humans.).
What are your examples for franchise-movies that somehow made the original worse?
Are songs on albums usually connected by lore and story beats? Not usually. That’s not a great analogy; very much apples and oranges.
Many albums are made around a theme or idea. Or at least that’s the way musicians I like tend to do it.
That’s still not how franchises are made though. They are often made based around specific plot points and lore, not just theme.