Colin Farrell gif!!!
I think it's safe to say that the Matrix sequels killed a lot of the enthusiasm fans had for the original itself. Hardly anyone talks about it like they used to. Back in 1999, this was literally the beginning of people being disappointed, ultimately, with the Star Wars prequels, because something new had stolen the zeitgeist.
Later seasons of Lost suffered the same fate; they ruined the hardcore love the first season engendered, because they did things fans didn't really want, in ways they didn't really want, until the big flash-forward twist, and then the series did it again with the final episode, and now you don't really hear anyone talking about how awesome any of it was.
But it's not as if everything that's massively unpopular in later installments will do this; Superman III and IV, the varying levels of disinterest and/or massive hate of the three movies that follow it don't leave 1989 Batman in the dustbin, The Dark Knight Returns is still loved despite Miller's later perceived misfires, the Ultimate line isn't dismissed despite a fairly wretched fate...
There are degrees to this, depending on how big the later changes are, how much they diverge from what originally made something popular. But it also works in reverse, such as Star Trek II: The Wrath of Khan, which is widely considered the savior of that franchise, making sweeping creative changes that were enthusiastically embraced.