Thoughts:
No leveled encounters. I know the choice is typically between leveled and zoned encounters in RPGs, but I think there's an overlooked 3rd option in basically making the combat difficulty static the whole game -- setting the entire system to be based around skillful gameplay and high tech gear and implants instead of heavily reliant on combat skills system (obviously adjustable with a difficulty slider for people who don't like to suffer). The difference in encounters would then be the number of enemies, or the gear of enemies, rather than the level or skill of enemies (this could easily have organizational or faction ties as well... which could make things semi-zoned without being too restrictive). This lets the player free roam the world from the beginning, but also not feel punished by the world for "leveling up". The skill system should be focused more on tactical advantage and extra-combat game features rather than firing accuracy and gun damage (things such as environment manipulation, hacking, stealth, tech skill, etc...). A gear/implant heavy progression system is still rewarding (in many games it is THE progression system, while the underlying level system is nearly semantic).
Honestly, that sort of reflects the cyberpunk pnp system fairly well in a game environment. In PnP you didn't really ever get to the indestructible point, and extraordinary survivability came at the cost of humanity (not to mention a lot of money.. lol). Having to choose your encounters, giving the player the option to run away from encounters when necessary, and making the combat more about creative problem solving, tactics, and gear, rather than leveling and skills makes the game challenging the whole way through while also providing the sense of freedom that people are nearly willing to sacrifice gameplay in general for (it also makes gear the progression standard so the player doesn't feel completely static). Terrain and tactics were absolute KEY in cyberpunk pnp. Honestly, the best way to compromise the two if you wanted to make skills affect combat, would be to make them affect gear, stealth, and mobility, instead of shooting/aiming/damage/defense ratings.
Also, cyberpunk is a strongly party oriented system. It's a prime candidate for adding in a 2-4 player local/session coop campaign if I ever saw one (which a lot of people would love to see in an open world rpg finally), but even if you don't want to do that, you should at least add an extensive companion/mercenary system. This also allows the full roll implementation, and class choice to be meaningful without players feeling completely punished for playing a less combative class, as they can just hire on mercenaries or companions to lessen their inherent weaknesses a bit if they want to play a less combat oriented class. Really, the only other choices would be to water down or omit the classes to where every character could potentially do everything... In other words your character options boil down to super soldier or a super soldier with a different looking face. That kinda kills the mood of the setting in general and makes the replayability drop a bit.
In my opinion, It is incredibly important in cyberpunk to have full jack-in netrunning. Not just hacking security cameras and doors or making netrunners some sort of lame robot pet class. To do a proper cyberpunk game, it basically has to have a secondary cyber world within the overarching game (which is, admittedly, a LARGE undertaking). Some people would argue that this basically is content that only netrunners will ever see, but with the inclusion of a merc/companion system, you could easily get past that a number of ways. On top of that, it is a system that lends itself fairly naturally to procedural generation, so it can be massive without being painstakingly scripted out and without sacrificing immersion or feeling like an empty system. Also, if it is heavily procedurally generated, it is much more justifiable to make it optional content, to where you could spend tons of time there or never even see it apart from an occasional side quest (where you could just hire a netrunner to access the content). In the canon there are ways to jack in without being a dedicated netrunner using a piggybacking system where a netrunner brings you along for the ride, so it isn't without precedent for a solo or fixer to join their team mate in a net run -- they just wouldn't be in their element, and their roll would switch to a support player instead of the leader being supported. The system would basically be paying for effectiveness and how much they want to spend on netrunner rates (basically having the choice to hire a legit cybercowboy or go cheap and struggle through the run with a crappy wannabe with bad gear). I think this is a pretty good solution to still being able to see content without being a jack of all trades. It also makes a netrunner centric character still have major advantages in their forte, since when playing as one you would have full control over their gear and implants, as well as being able to jack in whenever they want and take on the more demanding runs.
A first person OPTION would be nice as well, for those of us that like the immersion that comes with riding inside a virtual body. And since the game seems to be goaled towards creating a character instead of playing an established character, it is less objectionable. But that is just icing.
Finally... just stating the obvious, lol: this game should never even come close to being an MMO... nor should it include any of the gameplay of one -- No hotbar, no click target, no faux turn based combat, no ability cycling rotations/ cooldowns, no MMO "endgame" grinding, no level grinding, no farming, no fetch quests or kill 6 sewer rats... I could honestly do without gear crafting in general (though gear modding could be cool). I have faith in CDPR to know I don't really have to say that, but it is a friggin compulsion at this point.. lol
TLDR version -- Make it cool.
