Okay, lets get a few things straight.
His passive is what defines the champion. It takes a lot of time to master the bush jumping mechanic, and is only abusive if you don't know how to play around it. Getting outplayed by this mechanic is exactly that: O U T P L A Y E D. Making it only apply to Q would make him nearly unplayable, as it would remove the auto-attack reset from his kit while making him completely immobile.
Removing his passive would be like removing Katarina's passive: it would COMPLETELY DESTROY the champion, as their ENTIRE kit revolves around it functioning the way it does.
Alright, so why don't we just remove the Fury effects from Renekton? Or the heat effects from Rumble? WHEN THEIR MAIN SOURCE OF DAMAGE COMES FROM THEIR RESOURCE MECHANIC, REMOVING IT MAKES NO SENSE. The only reason he's able to deal damage AT ALL is because of his Ferocity. Just try to combo someone while ONLY using your basic 3 abilities, ESPECIALLY if you can't reset your auto-attack with your Q because of your stupid idea to only apply his passive to his Q.
His empowered effects give him SITUATIONAL benefits depending on what he wants to use. He can't use all 3 at once for obvious reasons, since you seem to be looking at them all at once.
Let's start with his Empowered Q. This gives him extra damage, another Q, and attack speed. This is strong for bursting someone, but if he isn't building glass-cannon it won't allow him to 1 shot someone. If he IS building glass cannon, and he uses this, he'll be vulnerable to getting bursted himself.
His Empowered W gives him a heal and extra resistances. Sounds great, except if he uses this, his damage is garbage because he has no AD and AA-Speed steroid and no extra Q.
His Empowered E gives him a snare (NOT A STUN), which is a dodgeable skillshot that has a relatively short range and decently slow travel-time. Unless he's landing this mid-air, it's pretty easy to dodge. If he IS landing this mid-air, he wont have enough damage left to burst you with, because (again) he has no AD and AA-Speed steroid and no extra Q. If this is your biggest problem, you can ask your support to buy a Mikael's Crucible or get a QSS and you will win easily.
BUT currently his E is completely bugged to go in some random direction whenever you try to cast it mid-air, so you shouldn't even be having this problem.
Honestly, either of your changes would gut Rengar to unplayability, with no regards to balance what-so-ever. Just because you got beat by a Rengar once or twice doesn't mean you know a single thing about changing him.