Full Reworks aren't for the Champion's Fans
First, it's important to note the exceptions; the reworks that leave most abilities the same. Ezreal and the upcoming Morgana rework are major outliers from the trend I'll be addressing. That's because they're popular, and the aspects of their kits that need(ed) reworking weren't their core features. Ezreal's entire kit has proved able to stand the test of time, but his W was neither core to his kit nor meshed well with the rest of it. Likewise, Morgana's passive and W, one being a stat that's now considered unfit for mages and the other being an ability that entirely relied on that stat, also don't mesh with the rest of her kit but aren't (or, aren't any longer) core to it. According to the recent roadmaps, they'll be aiming towards making her kit more conducive to using her ultimate effectively.
With that out of the way, I'll get to talking about full reworks. When a champion needs a full rework, it's because their entire kit is either outdated or extremely difficult to balance. The abilities that fans of the first iteration are fond of are the problem that needs to be fixed. They can keep the more general themes or certain parts of abilities, but most of the specifics have to be changed.
Sion is probably the biggest example for the first case-- outdated kit. For Sion, they were able to keep his permanent health gain and W, but not the rest of his kit. His passive functioned too similar to Dodge Change, which they deemed unfit for the game. The same goes for targeted non-ultimate stuns like his E (Taric's another example). His E and R were essentially passives, forcing him to rely on auto attacks without any AD scaling on his abilities despite having one of the shortest auto ranges. His original design leaned heavily on the idea that Ability Power means only abilities and Attack Damage means only auto attacks. So while his fans may have liked his really high AP scaling on Q and W, it didn't make for fluid kit.
Aatrox, being the reason I felt the need to type this thread because people are still talking about him, is an example of the latter-- extremely difficult to balance. His kit wasn't outdated as it wasn't much different from other auto-attack based fighters, being especially similar Xin Zhao. But he was always either the best or the absolute worst choice among them. Usually the worst. It is a shame that the highest point in his history (Conqueror's overpowered introduction after he got his W's health cost removed) came right before his rework was finished, but it was yet more evidence that he was difficult to balance. The problem wasn't that he couldn't be made good, it's that he couldn't be made balanced. He either had too much sustain for the damage he dealt, or couldn't have enough sustain in exchange for damage. And that was core to his kit. If anything, the fact they just hacked off his healing against minions is further proof that his old main strength was unfit for the game.
Yorick is, in my opinion, the best rework (not that I love Yorick, but in terms of how the rework was handled). Because he was an example of both an outdated design and a difficult to balance one, but they still managed to keep almost every aspect of his old kit. He completely relied on poorly designed pets, resulting in a passive playstyle that didn't suit the shift to more active play (other examples of this include Sona's rework and the changes to support items). But when it was strong, there was effectively no counter to it. The varying effects and summon methods of his pets, their difficult-to-click hitboxes, and his semi-revive ultimate, all things old fans likely appreciated about him, needed to be changed. Yet he still relies on pets, still has his auto-reset, still has an AoE slow, and still makes a stronger pet for his ultimate.
When very few people actually play a champion, keeping a champion too similar to their old iteration when they're reworked doesn't fix anything. And that usually means the things mains love about the champion, Sion's AP scaling, Aatrox's on-hit healing, Yorick's unbeatable ghouls, Warwick's targeted suppress, Taric's hammer slam, Akali's targeted dash, Poppy's invulnerability, etc. are what gets targeted for change. They're trying to broaden the playerbase while making a modern, balanced champion. They may not always succeed when it comes to balance, but they do try to make a kit with the flexibility to be properly adjusted.