This stuff flew over the head of 95% of people who played it. That and the unrealiable narratorness of Johny.
Yeah, I liked how they handled Johnny as a character. Alt explicitly points out the construct's deranged, self-deluding nature, and his flashbacks really drive home just how much of a narcissistic, violent psychopath he really is. It was amusing picking his most egotistical, megalomaniacal responses because they fit.
If this was their intention then they did a poor job of presenting it. You first hand over control during the
"Chippin' In" side quest where you'll see the super cut. This leads to the next side quest
"Blistering Love" where you already have direct control over Johnny and this happens within two ingame days. There is no gradual build up, no comment from V that he now sees more when Johnny is in charge, nothing. Also, if V is your character, should you even be able to play Johnny at all? Him taking over control should lead to less control instead of more. Given the state of the game it is hard to be sure.
That's the point, Johnny's an NPC when you start out, which is why the first sequence is non-interactive, but as he overwrites more and more of V, he's gradually becoming the PC right under the player's nose, so the player gets agency over his choices. You're outright warned that this would happen by one of the other NPCs, I forget which, that the Silverhand construct acts as a virus and will eventually ask you to voluntarily surrender more of yourself to it under various pretenses, and if you choose to do that, the player's growing degree of agency over Johnny is meant to mirror's V's diminished state.
This is the narrative designer folding the cyberpunk literary motif of identity into the videogame design concept of Player-Player Character identity. In a general sense, what you see happening to Peralez from an external perspective you also see happening to V, but first hand, internally and underlined by the resulting gameplay implications. It's a smart move and one of the stronger points of Cyberpunk's design because it renders a constituting literary theme at the interactive level. The pacing isn't optimal, yes, but that criticism's true of the entire game.
You could do things the other way around, like you suggest, with the player exercising less control over the protagonist the more Johnny takes over, but it would be a weaker representation of the subject matter - the Silverhand construct isn't a rival to
the player, but to the player
character, to V. And, as V, the idea isn't that you're losing
control of yourself, but that you're losing yourself altogether, becoming someone else. Thus, the end point of the engram takeover succeeding is that the player is still in control of the protagonist, but that protagonist has changed, and the way CDPR have chosen to portray that is subtle but effective.
You start out holding a can of orange soda. The more you drink from it, the taste changes. You're still holding it, it's still your can of orange soda, but by the end it tastes like lemon-lime.
P.S. There's a flipside to this in a different department, though I've yet to finish the game and confirm. If I got it right, engaging with the side content is also contextualised in the scope of Silverhand's influence? If so, it's a bad call from both a writing perspective, a mismatch with Silverhand's character, and a design one, seeing as it retroactively deprecates player agency à la Bioshock. "Would you kindly" is a great twist for a book or movie, but a massive misstep for a videogame.