My biggest problem with the game is just how obvious it feels that this game is several different versions of the game stitched together into a sort of Frankenstein's monster, leading to a lot of noticeable cut content and feeling that a lot of nonsensical elements probably made more sense in a previous version of the game.
- I feel like there's a version of the game wherein your choices were meant to affect how much control Johnny Silverhand has over you and how quickly the 'change' in your brain and body happens. I think your introduction to him supports this: he's set up as an antagonist that wants to take control of your body. Yet after that scene the idea that he can take control without you first giving it up is largely dropped and he's written far less antagonistic towards V.
In early quests once you're stuck with Johnny you're given choices to agree with him and act like him (e.g. smoking) or to reject him, and even cut conversations with him short by taking the omega blockers. These choices mostly disappear the further you get into the game and the choices that are there don't seem to impact much of anything.
Tying into this is the 'meditation' quest-chain with the monk. If the game did track how much control Johnny has then a series of side quests wherein V finds inner-peace and centers himself could have been a way for players to lower the 'control' stat. In the game we got, though, these meditation quests seem to serve no purpose and have no payoff.
The game does *appear* to track how friendly you are with Johnny but I'm not sure what all affects this. I always told him to fuck off and took the omega blockers when I could yet the game acted as if we had become true bros by the time of act 3. I'm not sure if how the game tracks this is buggy or if the developers just didn't put in an alternate set of scenes that reflected a bad relationship.
- The main story quests and the rest of the game feel at odds with each other. According to the main plot Arasaka thinks you killed their leader and stole an important prototype from them. Yet nothing ever actually comes of that outside of the handful of main story quests that deal directly with Arasaka. Being hunted by one of the most powerful corporations in the world never seems to affect any side quest nor are there any side quests that deal with stuff like, say, them sending a kill squad after you or having to deal with an assassin that they hired.
Then there's also the Voodoo Boys. Much like Arasaka they feel like they barely exist outside of the main story quest-chain that deals with them. Even after they fucked me over twice during their quests I left them alive because I figured they'd surely have some sort of content tied to them or I'd be able to call in a favor during the ending. But, nope, they never showed up again.
Lastly there's the cyberpsycho quests. The game's main plot deals with V inserting a cybernetic implant and it fucking him up. The cyberpsycho quests deal with the eye-patch lady wanting to research how cybernetics can fuck up people. I feel like the connection there is too strong and obvious for it just to be a coincidence. Furthermore, this quest-chain has no real payoff; I managed to keep all the targets alive and all I got was a quest to meet the eye-patch lady in person so she can basically say "Good job, buddy. Thanks." and that's literally it, which is to say that whatever originally planned conclusion to this bunch of quests likely got cut.
- The side gigs feel weird. This observation I'm less confident about but I feel like each fixer was meant to have their own quest chain with the gigs tying together and leading to a final mission for each fixer. The only evidence I have for this is that each fixer has an NPC you rescue that gets their own entry into the database and who then sits around next to the fixer for the rest of the game, as if they were meant to be important and have some sort of content, and yet those NPCs are never tied to anything else. Then there's also the fact that the Padre is given a connection to streetpunk V that never goes anywhere.
- Finally, it's obvious the game they were working on as late as 2019 was majorly different than one we got. Like this
article that talks about the police system. None of the game's systems are nearly as in-depth as described there. The article also hints at a system that tracks V's reputation with NPCs but, again, there's nothing like that in the game.