I wonder what happens if I follow this to what I viscerally feel to be a supervillain: Death itself.
Maybe Death is like Gaddafi. It is very bad, but gives a semblance of order, and removing that might not make living in its former domain any better immediately. It is hard to even make a guess at the probability of this, given that we don't know what defeating Death would mean or even look like, but we can try to build scenarios and select among post-villain worlds before its removal, in the same way that we and the Libyans would wish had been done in the Gaddafi case.
Do we want to retain Death as an option? Or should immortality, once accepted, be compulsory? Fictional immortalities tend to not be absolute: if you wanted to kill yourself, you could still jump into a black hole or something. But suppose those aren't possible, and a more modest type of durability can be rounded up into immortality by some cognitive modifications that create extreme aversion to bodily harm. Even if those didn't necessarily come with durability, people in love could still blackmail each other into accepting such modifications, and spend billions of years living a life that isn't actually a choice, sort of like in Friendship is Optimal.
Then there are the innumerable ways immortality could be worse than death - many of these have already been explored in fiction. Maybe you permanently lose 1% of your capacity for reason and happiness every 50 years, and unlike Death that isn't fixable - or whatever.
But even if both of these were averted and immortality was otherwise perfect for the immortal individual, it might still be a bad thing for humanity or life. If it is not available to everyone - because it is too expensive, classified as Top Secret military technology or only works on people with certain inalienable features like particular chromosomes or a Wizard Gene - that gives a whole new level to societal inequality. Death used to be the great equalizer - remove it and the rich (or Wizard Gene holders or whatever) become so dissimilar from mortals as to be practically a seperate species. And the only comparative advantage mortals retain is the ability to do suicide attacks. That kind of scenario can go wrong in all sorts of ways. It can still be a net gain for a select group of individuals - like getting rid of Gaddafi was a net gain for the people in his prisons - while a net loss for a larger number of other individuals.
You could construct even weirder scenarios, where immortalizing one individual removes one distant and probably lifeless galaxy, but I find it too hard to suspend my disbelief about such scenarios for them to help me think.
So how would removing Death lead to a certainly improved universe? I think that at a minimum, it'd have to be available to every human, retain Death as an option and not have side-effects that could ever escalate into fates worse than Death. That's a much, much taller order than "just invent uploading and declare victory" and might be a hopeless endeavor even if uploading is possible.
After going through these imaginations with something I viscerally feel to be a villain, I can kind of understand the impulse to just remove Gaddafi and hope for the best, rather than plan (and take responsibility) for what happens after.
We have a recurring theme in the greater Less Wrong community that life should be more like a high fantasy novel. Maybe that is to be expected when a quarter of the community came here via Harry Potter fanfiction, and we also have rationalist group houses named after fantasy locations, descriptions of community members in terms of character archetypes and PCs versus NPCs, semi-serious development of the new atheist gods, and feel free to contribute your favorites in the comments.
A failure mode common to high fantasy novels as well as politics is solving all our problems by defeating the villain. Actually, this is a common narrative structure for our entire storytelling species, and it works well as a narrative structure. The story needs conflict, so we pit a sympathetic protagonist against a compelling antagonist, and we reach a satisfying climax when the two come into direct conflict, good conquers evil, and we live happily ever after.
This isn't an article about whether your opponent really is a villain. Let's make the (large) assumption that you have legitimately identified a villain who is doing evil things. They certainly exist in the world. Defeating this villain is a legitimate goal.
And then what?
Defeating the villain is rarely enough. Building is harder than destroying, and it is very unlikely that something good will spontaneously fill the void when something evil is taken away. It is also insufficient to speak in vague generalities about the ideals to which the post-[whatever] society will adhere. How are you going to avoid the problems caused by whatever you are eliminating, and how are you going to successfully transition from evil to good?
In fantasy novels, this is rarely an issue. The story ends shortly after the climax, either with good ascending or time-skipping to a society made perfect off-camera. Sauron has been vanquished, the rightful king has been restored, cue epilogue(s). And then what? Has the Chosen One shown skill in diplomacy and economics, solving problems not involving swords? What was Aragorn's tax policy? Sauron managed to feed his armies from a wasteland; what kind of agricultural techniques do you have? And indeed, if the book/series needs a sequel, we find that a problem at least as bad as the original fills in the void.
Reality often follows that pattern. Marx explicitly had no plan for what happened after you smashed capitalism. Destroy the oppressors and then ... as it turns out, slightly different oppressors come in and generally kill a fair percentage of the population. It works on the other direction as well; the fall of Soviet communism led not to spontaneous capitalism but rather kleptocracy and Vladmir Putin. For most of my lifetime, a major pillar of American foreign policy has seemed to be the overthrow of hostile dictators (end of plan). For example, Muammar Gaddafi was killed in 2011, and Libya has been in some state of unrest or civil war ever since. Maybe this is one where it would not be best to contribute our favorites in the comments.
This is not to say that you never get improvements that way. Aragorn can hardly be worse than Sauron. Regression to the mean perhaps suggests that you will get something less bad just by luck, as Putin seems clearly less bad than Stalin, although Stalin seems clearly worse than almost any other regime change in history. Some would say that causing civil wars in hostile countries is the goal rather than a failure of American foreign policy, which seems a darker sort of instrumental rationality.
Human flourishing is not the default state of affairs, temporarily suppressed by villainy. Spontaneous order is real, but it still needs institutions and social technology to support it.
Defeating the villain is a (possibly) necessary but (almost certainly) insufficient condition for bringing about good.
One thing I really like about this community is that projects tend to be conceived in the positive rather than the negative. Please keep developing your plans not only in terms of "this is a bad thing to be eliminated" but also "this is a better thing to be created" and "this is how I plan to get there."