One of the few Villain replacements I can remember is that of the old man Adrian Toomes Vulture, when his prison cellmate a younger man, Blackie Drago tricked Toomes into believing he would soon die so that he could steal the Vulture suit and use it for his own criminal schemes. He of course fails and soon is teaming with Toomes until is humiliated and defeated. Later on in the world of Spidey another takes on the name of Vulture, Clifton Shallot becomes an actual mutated Vulture of sorts with real wings and claws. Then there was the time a group of felons use the Vulture flying harness design to become the Vulturions until Toomes finds out and defeats them all. They have been seen here and there about since committing heists. Jimmy Natale becomes a Vulture vigilante going around killing and eating criminals while going after the mobsters responsible for causing his transformation. 

Later on in Spidey #63 when the 2 Vultures team up it is explained that Drago caused the accident which weakened Toomes and was the cause of his "dying" but in actuality when Toomes learned of Drago's fight against Spidey, it angered him into a frenzy providing him with the will to live overriding his "illness" and weakness. Revenge is a powerful motivator! 

I loved the era of post-Batman RIP. 

Dick was a great Batman and made even better when he had Damian at his side as Robin.

I don't know the issues, only that they exist, but didn't Freddy Freeman become Captain Marvel at some point? (No, I won't use the name Shazam, it's a battle I wage eternally).

Gotta agree here that Dick Grayson should be the ONLY successor to Wayne as Batman within normal continuity until some time into the distant future. 

Robin though has been proven to show over time that just about anyone can put on the yellow cape and red breast but having Damian the "son" of the Bat does make the identity a bit more interesting. 

If you're talking about temporary replacements where it was clear it was temporary, I think Dick Grayson as Batman and Rhodey as Iron Man top the list.

While I love me some Kyle Rayner, that was never meant to be temporary, and of course he's still around as a GL after they foolishly brought Hal back. I've never thought of Kamala Khan as a replacement anything, she's a fan girl.... more a tribute. She's awesome though, if you want her to count

I also loved Hal as the Spectre (Though I realize not many do)... I kinda wish they stayed with that, it made SO much sense.

You could argue these days Beta Ray Bill is a better Thor than Thor is. With so many Thors now, though, it's almost a title.