For reworks that are design-driven, it usually comes from "if this character is ever good, he'd have to be nerfed." This analysis is driven by their play pattern, tradeoff set, and core decision-tree.
In Rengar's case, there were a few problems that made him not balancable;
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Rengar's stealth is extremely good at bypassing wards, peeling and other defensive measures. Combined with good CC and high burst, this meant Rengar's success was wholly dependent on this - with no respect to how he has to overcome obstacles, interact or have any way to modify the context of how he performed. This means Rengar does what he does, and if he's good at basic League play, you'll lose your MVP without much recourse (and therefore likely teamfights/lane).
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Rengar's was somewhere between "Fighter" and "Assassin." (Hint, if you ever see a class combined with another at the same time, instead of a choice between them based on build etc, then that guy is likely BS). His pattern asked you to build up, but his damage was that of a burst assassin - incompatible gameplay levers.
Scruffy has a couple more he was looking at, in the guts. I know there's some frustrating about Rengar because we changed him from an Assassin into a Fighter, but on these characters, a choice DOES have to be made.
The missing piece is that, if we'd chose Assassin, Rengar's Stealth would have disappeared, or his burst still lowered. To add reasonable decision-making and interaction, this incompatibility would have kept Rengar knee-capped forever, or would have invalidated other choices because you knew he'd get the job done without much uncertainty. Characters (yes, even Assassins) need context to be healthy.
So, we thought the Stealth and Hunter identities were MORE important than the power profile. The defining feature of Rengar is not "he bursts", but is instead his ult, resource mechanic, Bonetooth, and being an aggressive character. I still think that's the right choice looking at the alternatives (keep weak forever, or remove entire skills).
Changing power profiles is going to happen with almost every character that's overloaded - whether it's Grags, Xerath, Heimerdinger, or Rengar. One thing we learned a lot from on the Skarner rework was that while there will be things we need to remove for health, we need to make sure there's a reason that's EXCITING to play the character still - even if it's a different thing to be excited about mechanically (and in fact, we're going to go back a little on Skarner's changes as a result).