I don't disagree with what you are saying; but wasn't the whole point of the rework to create opportunities where Ryze is weak? Ie, when his passive is down (or far from being ready) that is the best time to fight him?
To talk about your comment that it is hard to control his passive; I have to disagree again. With Q on a 4 second cool down, Ryze has access to his passive very quickly; he can throw 3 Q's to hit nothing (or cs with them, or harass with them), and hold E, W until he is ready to engage. When he gets his R, he only needs two Q's. This means his passive is at his beck and call every 12/8 seconds, before you account for cdr (he gets a LOT of that for free). Remember, he doesn't have to land his spells, only cast them; his W, E, and R can't miss, and his Q stacks regardless of a hit.
As a result, Ryze only has to wait, at most, for two spell cool downs before he gets his passive. If one of those spells is his Q, his E will be up 3 seconds later (fairly quickly) and then he can return fire. The window in which an opponent must attack is so small considering any even semi decent ryze player will know this is their only weak point and back off enough to charge it again.
Ordinarily I would say this isn't a huge problem, but when you have a champion like Ryze, who can build VERY tanky, get sustain, and still output large amounts of damage (his calling card), I can see some problems arising. By letting him build his passive whenever, you seriously inhibit the enemy's chance to exploit the weakness when it is down, because that weakness is never really there.
Because of this, we are seeing his rapidly rise in the "this champ is OP" category and we can see Riot's response on the pbe; a response I think is the wrong approach to the problem.
I guess basically the TL:DR is his passive is SUPPOSE to have down time that enemies are suppose to take advantage of, because otherwise Ryze basically steamrolls your team. His current passive doesn't seem to support that sentiment that was part of the foundation of the Ryze rework.
EDIT: This was added as a very late after thought, but if you are going to compare ryze passive management to Gnar's, I think you are way off base for a few reasons. The first is that opponents can force Gnar's passive, something that opponents can't do as easily to Ryze. More important, and related, is the second reason; gnar's passive has a long cool down (between time you can't build fury and then actually building the fury again) where Ryze doesn't. A skilled ryze should hold his W and E near the end of his passive to just charge it up again as soon as he can; the lack of an internal cool down on the passive is what is pushing Ryze to be so hard to balance.
If Ryze passive were to change in such a way that it actually had a meaningful cool down between activations, then I think it would be okay to make it easier to use. For example, if the passive had a cooldown of say, 15 seconds between which it could be used, then I think the active management of the passive would be much more important. Stacks could decay one at a time (rather than all at once) and spell casts (not hits) could charge it. But again, this would only work if his passive wasn't so accessible the rest of the time, which it currently is.