The villain nearly kills the hero the first time they fight but in the second meeting, the villain is killed immediately.
The villain starts out being the main issue of the show, even episodes that didn't focus on him personally ended up being part of the plot to destroy him or part of his plans. In later episodes, he's no longer the only villain and preparation to defeat him takes a lot less effort.
The villain started off being on mostly equal terms with the hero, beating him after a hard fight. In the second fight, it ends in a draw. The third time, the hero barely ekes out a win.
The heroes get stronger and figure out more of the villain's weaknesses, giving them a better advantage.
The villain won last time but in but doing so ended up inflicting critical injuries to him and draining most of his resources, with any followers he may have had now dead, defecting, doing a Mook-Face Turn or simply in jail. He's going to go down a lot easier this time around because he has less.
The villain was going after the heroes instead of training and no longer learns new skills.
During the final showdown, a split-screen effect shows the first battle on one side (the past) and the current one (real time in-universe). A voiceover from one of the heroes points out the ways in which the two confrontations differed.
Zig Zagged: The villain goes from being a legitimate threat to a weakling on several occasions.
Averted: He keeps his menacing stature throughout the series, despite failures.
The writers plan on making switch sides or other circumstances that may change his villainous personality.
The writers don't know what to do with the villain to keep him relevant after he's defeated so many times.
Lampshaded: The heroes recall that the villain used to be such a threat, but turned into a joke as soon as they beat him the first time.
Invoked: The heroes wait awhile to rebattle a powerful enemy.
Exploited:The Big Bad purposely decreases the power of his minions to give the heroes a false sense of security before facing him.
Defied: The villain assiduously endeavors to remain as powerful as ever which includes learning from his mistakes and remembering to level grind.