Lee and Zac were already in the meta when Shyv dropped in. Vi and Hec only showed up to pick up their free LP off of colossus being busted as hell. Her rework is a big part of why she is strong now, the jungle changes did help her but she wasn't a popular pick until last patch, which was incidentally her rework.
Now before her rework she sat below a 50% winrate. This is with the majority of her players being dedicated mains. afterwards her playrate and winrate jumped, which implies that even newbies who are unfamiliar with her are winning. Moreover shes winning in a meta full of bully junglers and early gamers who are supposed to win the game before she even becomes relevant. She's a farm jungler excelling outside of her meta. There was no larger meta shift that caused her to be good.
The OP does a rough job of listing both her losses and gains, as with a bulletpoint list it just looks like it was a net nerf. However when you look at the value of what she actually gained versus the value of what she lost the rework fixed more of her problems. For example
-Shyv didn't have much of an issue being tanky before. She still doesn't but now her passive snowballs off of mid-bot map control which is easy once she gets ahead.
-Shyv did have issues not getting stopped mid ulti. Especially with things like Poppy and other cc tanks surging in popularity with colossus being as strong as it is, without her ult being changed she would perform much more poorly than she does now. Losing the damage on ult is meaningless here because half the time you got stopped before it applied to anyone.
-Losing missile speed on her e is big, but the speed was exchanged for range, persistent aoe, way more burst on the ability itself, and still retained its capability to mark multiple targets for her autos and q.
Yes her clear factors, and yes Botrk factors (even though it's the only core item on her that changed), but the meta shouldn't favor her at all, having a larger playrate almost always results in a lower winrate due to people first timing her. You can't just blame this on item synergy and a metashift where she should be hard punished for waiting for her midgame.
Funny how in a meta full of cc tanks, bruiser carries, and bully junglers abusing a mastery, the one rose to grow out of the concrete is a jungler with no cc or gapcloser pre-6, who farms and hits you with a sack of gold midgame. By that logic my girl Evelynn should feel right at home here. Looks up win-rate
oh...