Hey Repertoir, thanks for posting in a thread about this.
Here are my thoughts/answers to your questions:
1.) I feel that Kha'zix's evolution order is dependent on the compositions of both teams, as well as what role he is filling.
From a role standpoint: I don't like playing Assassins because I struggle with the Assassin playstyle; I'm much more comfortable playing Fighters. That said, Kha'zix's R evolution helps me emulate the Fighter style with him in top lane (by means of skirmishing and giving me a lot of all-in strength), and I can stand toe-to-toe against Fighters through early-mid game. His R evolution is a very viable option against Fighters, though sometimes I'll evolve Q first against Fighter players that are very aggressive and leave their minions often.
From a team composition standpoint: If I'm jungling Kha'zix, my first evolution will be very dependent on how easy ganks will be to pull off. If my team is frequently pushing hard (thus, there will be small windows of time to kill the enemy laner without using hard Crowd Control), then I'll evolve my R so that I can proc my passive's slow a lot during the gank and so I'll have a longer duration stealth to close the gap for the gank's surprise factor. If ganking will be easy (if my teammates let themselves be pushed in or have hard Crowd Control), I'll evolve E just to get in there right away and start dealing damage to secure a kill.
2.) Is his R evolution worthless? In my personal opinion, no. In the opinions of many other players, yes.
Again, because I love the Fighter playstyle, Kha'zix's R evolution is my favorite, because it allows me to skirmish with my target. And being successful with R evolution is mentally rewarding. I didn't just kill my opponent because they stuck around too long @ low HP and I was able to Wing-jump in for some burst damage (playing off your opponent's lack of skill/perception); I was able to kill them through skillful movements while stealthed, making frequent use of my passive's slow and bonus damage, and dodging my target's retaliation with the use of the stealth duration.
I think R evolution is less valuable to those who want to play Kha'Zix as an assassin, and more valuable to those who want to play Kha'Zix as a Fighter or a split-pushing duelist.
3.) Some things I think would be good/bad on the charge system for his ult.
The Good:
-There are cases where Kha'Zix often just needs to use one charge of stealth to dodge around an incoming gank or enemy retaliation, but then the enemies back off and there is no need to use the second or third charge. That feels bad. The charge system would fix this.
-It will give Kha'Zix players more versatility in how they use it. Know you won't need to use your ult for awhile? Use it for the movement speed to get back to lane faster, or between jungle camps. And if you just need one charge for a gank, then you can use the other charge(s) later for another gank. There are other possibilities.
The Bad:
-Counterplay against Kha'Zix will be harder. Cross-lane communications of "Kha'Zix ult down" will no longer be valid. You can no longer have the safety of knowing his ultimate is on cooldown. Which brings me to another point.
-The charge system will increase Kha'Zix's perceived threat. Because it's likely that he'll always have a charge available, who will want to engage him? Players will be less brazen against him, and it will make it harder for Kha'Zix players to actually pull off successful ganks/skirmishes.
I'm not sure whether the charge system or his currently evolved ultimate would be better. On the charge system, would the cooldown between consecutive uses be increased? Would the mana cost just be greatly reduced per charge consumption, or would it be free? Or would it stay the same O_O? What playstyle does the charge system cater to more?
Whatever the ramifications of the charge system would be, I'm definitely comfortable with where it is at. I like that it helps me play him like a Fighter, and I wouldn't want that to be taken away.