Warning: Long rant! I went on for a while on this subject matter:
I think the villains also have something to do with this. Superman III is a perfect example of this. With the first two movies featuring Luthor and the second with the Kryptonian criminals, they went in a totally different direction, with one-off villains. And as cool as the Superman/Clark Kent fight may have been (that and the "Badass" Superman may be the only worthwhile parts of the movie), it might have made the movie better if Luthor invented the synthetic Kryptonite, which lead to the creation of Bizarro, who could have fought Superman in the junkyard scene. Of course, there are more problems with the movie than just the villain.
As for Batman Forever, you can count me in the group that likes it, for what it was. However, I always felt that Jim Carrey's Riddler was too "Jokeresque." And Two Face was also over the top, even for a movie veering hard into the camp genre. A more serious Riddler may have made for a better movie and a chance to show off Batman's detective skills.
X-Men: Last Stand also did away with "big named" bad guys, but you could argue that X2 did the same, as Stryker is not a name the casual comic reader might know.
Spider-Man 3, I think tried to incorporate a villain which arguably did not work, as filmed. Maybe Venom could have worked better if, as the rumors stated at the time, we were going to get one "Black/Evil Spider-Man" movie followed by a "Venom" movie. The other problem is that they should have set-up Eddie Brock way back in the first movie, to have his "betrayal" by Peter have more resonance. Surprisingly, the villain that they did set-up, The Lizard, never came to be. After being mentioned in the first movie and given a key cameo in the second, the third movie probably should have used him, instead of the Sandman.
Focusing on the villains, I also think the emotional resonance with them dies down by the third movie. Superman and Lex Luthor are like Yin and Yang, so it makes sense that he'd be the bad guy in the first movie. The Phantom Zone criminals, being the only other Kryptonians Kal met at the time to have survived the destruction of Krypton also had emotional resonance. But, all of that resonance is gone in the third movie, so why should we care that Superman is going up against them?
The first movie is going to either use or make-up the villain to be the "ultimate" foe for the character. With Batman, we get the Joker, his antithesis. X-Men gives us Magneto. Spider-Man ties the Green Goblin into his origin tale and presents us with a dark reflection, two men given powers by science, with one using them for good and the other for evil.
The second movie must then try to make the villain equally important to the character. Thus, we get the Phantom Zone criminals, as I said. Batman Returns, in my opinion fumbles the ball here with Catwoman, but tries to show us how the Penguin, also an orphan, though through his parent's choice, instead of cruel fate, is a reflection of Batman. Stryker works due to his ties to Wolverine. Dr. Octopus is another character who gains powers in a lab accident similar to Peter and Norman, but they made him a sympathetic character and showed us how someone decent (unlike Norman) could easily turn, again showing us a reflection of Peter's struggles.
Two-Face and the Riddler really don't get much in the way of origins and thus, don't give us anything to hold onto. They are cyphers and that makes them uninteresting. Warren Worthington II, might have had some impact if they developed him and his son earlier and his plot to "cure" mutants developed over the course of the three films. The Sandman was shoehorned into Peter's origin in a way that rang hollow and I've already explained how Venom was shoehorned in. The less said about Harry, the better, except, again if they went with him as Hobgoblin and focused the movie on him, it might have made it better.
It could have worked if the movie was solely "Black Goo Spider-Man" and Hobgoblin going at it, and maybe Peter killing Harry (to contrast with him being blamed for Norman's death, which was not his fault, well, as far as jumping out of the way of his own imminent death could be his fault). The guilt could have driven him to realise it was the costume that pushed him to do this, and then end the movie with Peter divesting himself of the costumed, and a fully developed over the course of the three movies, Eddie Brock becoming Venom in time for Spider-Man 4.
Similarly, the Phoenix, which I've avoided talking about so far could have, again, been a whole movie by itself. And again, it would have had more resonance with us than it did in X-Men: Last Stand.
So, in addition to everything else we've discussed, I truly think the villain of the movie adds to the failure of the third movies.