Interesting difference though between a sequel ruining the franchise "thereafter" or being so bad it actually ruins the franchise retroactively.
Lots of bad sequels.
Alien 3 mentioned by Porkchop is a good example (you can lump
Predator 2 in there), but those didn't ruin the greatness of the originals for me. Ditto for
Lethal Weapon 3 or
Escape from LA or
Major League II.
However, I totally agree that the
Matrix sequels kind of retroactively killed the joy of the original to me. :(
Interesting question as to who had the bigger fall from early greatness/potential to mind-numbing failure:
The Wachowskis (
Matrix...then two Matrix sequels and
Speed Racer and
Cloud Atlas and
Jupiter Ascending...not sure where to classify
V for Vendetta on that list)
or
M Night Shyamalan (
Sixth Sense and
Unbreakable and
Signs...followed by
The Village and
Lady in the Water and
The Happening and
The Last Airbender and
After Earth)
Not trying to

. Just a thought...