I believe that the end of Dark Empire II or Empire's End showed that the Clones were actually being purposefully ruined by someone, which was then explained in.... Crimson Empire, I believe, the sequel to the Dark Empire trilogy.
It was Carnor Jax who sabotaged the clones (bribed the clonemaster, iirc) at the behest of his master, Lumiya. He used this opportunity to assert his own claim to the Empire, where he almost allied with Nom Anor before meeting his unfortunate end by way of Kir Kanos, the Imperial Kyle Katarn.
Interestingly, the transition of power from Emperor* Carnor Jax the Imperial Interim Ruling Council on Ord Cantrell afterward is where, imo, you begin to see the first real distinction between 'good' and 'evil' Imperials in the upper echelons. The IRC even had non-human members (albeit distinctly of the 'evil Imperial' strain), something that even Pellaeon at his most mellow and sagacious couldn't quite manage.**
Xandel Carivus, who came to lead it, pulled hard in the other direction and had the non-humans executed before declaring himself Emperor... whereupon Baron Ragez D'Asta, a member emeritus of the original (non-Interim) Ruling Council and a corporate magnate rich enough to own a personal military, tag-teamed with Kir Kanos to end his mockery of a reign before it got out of hand.
D'Asta then did something very significant: he signed a truce with the New Republic and let the true Empire
die. This event marks the end of Imperial legitimacy*** and the start of what would come to be known as the Imperial Remnant, though no cohesive government of any sort would exist for another year until Daala's masterful feat of diplomacy at Tsoss Beacon.
...because nothing quite says "legitimacy" like Tsoss Beacon, amirite?
* Though Carnor Jax clearly saw himself as the new Emperor, it's unclear if he actually got around to 'talking the talk' in addition to 'walking the walk.'
** I don't mean to write a hagiography of Pellaeon here, but it's clear that he found new perspective in his post-Thrawn career (perhaps helped just as much by witnessing firsthand the failure of so many other True Believers and ruthless successors) and genuinely became an advocate for and implementer of good governance. That said, his Remnant did remain very humanocentrist -- with the possible exception of Chiss brought in from the Empire of the Hand -- and it's not a good look. Still, to be fair, the worlds held by the Remnant were largely inhabited by humans, with a mere handful of exceptions, and those that were within their borders were treated well. For instance, Pellaeon brought an end to slavery of the Yaga and brought them into the fold as willing partners.
*** The true Imperial lineage goes like this: OG Palpatine → Sate Pestage → Paltr Carvin → [Isard or Trioculus or Shadowspawn or Dangor] → Thrawn → Asshole Palpatine → Carnor Jax → Burr Nolyds and the IRC → Xandel Carivus → extict after the Truce of Orinda.
