I love Cyberpunk 2077 but… I largely agree with you. Cyberpunk 2077 aims to portray a world where “a stray bullet could end you while hailing a cab”. The core issue is that the moment-to-moment gameplay Cyberpunk (I think) intends to provide – a relatively “realistic”, fast-paced shooter doesn’t mesh well with a level-based, stats-driven progression system.
Designing good shooter gameplay with fixed stats, for just one playstyle (cover-based, Doom style, stealthy, with melee weapons, etc.), is already not easy. The guns should feel distinct yet balanced, the enemies should be varied and challenging, movement should feel good, combat should have a good flow, the time-to-kill should feel right, etc. And Cyberpunk offers not one but 4-5 playstyles. Making all of them feel good is already a tall order. Not to mention the 4 different difficulty levels. But balancing all that out with a level- and stats-based progression system like Cyberpunk’s on top must be almost impossible. Your level, attributes, skills, and perks drastically change your hit points, gun damage and recoil, movement speed, the relative level of your enemies and your guns, all of that overshadows much of everything.
The level scaling system is probably the biggest culprit here. And I guess it's no surprise that the most popular mods that change combat eliminate the scaling altogether. Combat feels much more consistent. You can actually keep using the gun you like (without spending an increasingly obscene amount of resources to keep it up-to-date). You can go everywhere and have a good time. I didn’t feel like I was missing out on anything here. Personally I wouldn’t mind seeing the abilities and perks system gone as well, as it adds little for me, but at least the player can distribute points in such a way that it at least doesn’t detract from their experience.
I don’t believe the abilities and perks are going away anytime soon, but I do hope that CDPR adds a “shooter mode” that removes scaling altogether, maybe as part of the NG+ update. If solo modders can already get that to work reasonably well, that shouldn’t be too much effort. And it’s not like there wouldn’t already be other, more interesting progression systems in the game anyway: First and foremost cyberware, but also expensive weapons and gear, street cred, or thematically fitting loot during or as reward for missions (Arasaka gear from The Heist, for example, or Overwatch from Panam). If CDPR wants to go the extra mile, just expand them a bit.