I can see where you are coming from, but I don't really agree there for the most part. Sometimes, but only when it comes to certain villains, usually ones that are presented as basically irredeemable, which Doom was not.
Mostly because villains are by definition guest stars in a protagonist's story, they are there to give the hero something to fight against. While the best villains have motivations you can understand even if you don't agree with them, and they see themselves as the heroes of their own story a lot of the time, they are still there to serve someone else's story most of the time. This means that villains are a LOT easier to create new ones of, you don't have to keep the same ones around, because most people are reading for the hero, not the villain. Not every new villain will capture the imagination, sure, but there is always the next arc. And while some villains are interesting because of a deeper connection to the hero, I don't think that means the connection has to remain always the same. Look at Thor and Loki, since that is the one I know best. First off, Thor has not exactly been lacking in the villain department for the past 10 years with Loki no longer in that role of primary antagonist, there have been new ones like Gorr, and old ones brought back from obscurity like Malekith, and I don't think the stories have suffered because he isn't fighting Loki again. And they have been able to mine that relationship for more drama now than they would have been able to in the past, different kinds of drama, and they are apparently working together after WotR concludes, which should be interesting. So they may have lost him as a villain, but he is still a part of Thor's story, his supporting cast. And Loki himself is more viable as a character now than he was before. He's getting his second crack at a solo, (third if you count JiM. And both of them ended for plot reasons before, not because they weren't selling) you think they would have been able to do that if he had stayed a mustache twirler constantly plotting to attack Thor in some way? So the net result there was additive, new villains for Thor to fight, the relationship with Loki is still there, it's just different, and they have a 'new' character that can sustain a book.
Much the same situation with Magneto and the X-Men, though he is still a villain sometimes. But the walking the line between hero and villain rather than full on villain has in general resulted in more interesting stories, and he has the ability to carry his own story now in a way that he would not have been able to before Claremont made him more sympathetic.
And all of that could have applied to Doom as well, quite easily. Him turning face didn't have to mean losing him as a supporting character in FF, it just meant the exact way he participated would have changed. And the change could have exposed new facets of both his and Reed's characters that we haven't already seen repeatedly.