None of these series are my all-time fave per se, but they are excellent examples for the topic.
The Matrix- LOVED the first film. Liked the second one- it wasn't perfect, but it was pretty good and had one hell of a cliffhanger IMO. Then the third one came along. Every loose end from the second film was resolved in the worst/stupidest way possible, and the ending was the worst possible way the trilogy could have ended. It's like the second film backed them into a corner and they were like 'Okay, there's no way we can come up with a good ending that resolves everything, so let's just throw shit against the wall and hope it sticks'. Not only that, but Path Of Neo (the game) hammered further nails into the coffin. The extra stuff they added to the story/world was boring, unnecessary and downright stupid (kinda like Lucas' revisions to the original Star Wars trilogy

), and the re-edited movie scenes were incomprehensible garbage. Enter The Matrix wasn't a brilliant game, but at least it added some important things to the story (ie. tying it in with the Animatrix, developing the characters of Ghost and Sparks after they only got bit parts in the films). Path Of Neo just ruined those great memories, and the gameplay sucked as well.
Pirates of the Carribean- LOVED the first film. LOVED the second film- wasn't perfect, but it was loads of fun, had great action and had an AWESOME cliffhanger IMO. Then the third one came along. Every loose end from the second film was resolved in the worst/stupidest way possible, and the ending was pretty underwhelming. On top of all that, they spent the entire film adding new story threads that either didn't go anywhere, were completely unnecessary, or were completely stupid. I hope the fourth one goes back to basics and recaptures what made the first two great (not holding my breath though).
X-Men Trilogy- LOVED the first film, LOVED the second film... see a pattern here? The third film had decent action, but was terrible in many ways. Midi-chlorians in Star Wars weren't half as bad as those lame-ass uber-geeky references to mutants having 'levels' on a scale of 1-5. Main characters were killed/cured left, right and centre, which can be a good thing if it positively affects the story, but in this film it seemed like they were only doing it for shock value because they had no other ideas. Some of the deaths were barely even acknowledged, like when one of the characters said 'You killed him!' in an off-hand remark (I won't say who got killed so as not to spoil it) and you're like 'Wait a sec, I never even realised he was dead!' and it's never even mentioned again. And this was for one of the main, MAIN characters! Rogue's and Angel's storylines were used as filler but never developed into anything meaningful and never even got resolved- hell, the only reason Angel is in the movie is for that stupid Deus Ex Machina at the end, and they could have easily done that with any other mutant, so his presence in the film is completely unnecessary! Overall, the script was utter garbage, but at least the special effects were nice.
Blade Trilogy- Admittedly, this one doesn't really have a continuous storyline/canon like the previous examples, but I still thought the third film did irreparable damage to the franchise. First film was cool, second film was absolutely amazing (by action movie standards, of course), but the third one was an absolute joke. I could tolerate that lovely close-up of Ryan Reynolds' pubes, I could tolerate him trying to set a world record for the most needlessly profane scene in the history of films (because it was kinda funny), hell I could even tolerate the idea that his character used to be a vampire but had turned back to being a human (which is stupider than midi-chlorians!). But one thing I could not tolerate was a vampire hunter who magically drew her powers from listening to an iPod at full-bore during every fight. The idea that blocking out all of the surrounding noise makes you a better fighter is completely retarded (surely vampires could just sneak up on her from behind?), and I cringed when one of the scenes in the pre-climactic-fight montage was her tweaking a setlist in iTunes. This was the worst case of product placement I've ever seen in a film, but it wasn't even as bad as the fact that the Nightstalker's compound was destroyed because they left a BLIND person watching the security cameras! And the vampires just walked in and ransacked the place! Who the hell is stupid enough to leave a blind person on guard duty ffs? And Triple H as a vampire? No. Just no. After two fairly intelligent and interesting action/fantasy films, the third one sought to be the dumbest film in the history of cinema, and killed any hope of this otherwise excellent franchise going beyond three films.