I'm hoping for the following though I haven't played the PnP version.
Traits
Like in Fallout 1/2, you can choose 1-3 traits which define your character. Traits have a big bonus, but also a big negative. These can only be selected on character creation and lasts for the entire game. Unique traits can be obtained through some quests. An example could be that you run 25% faster, but take 15% more damage from all damage suffered. Or that you reload a lot faster, but also miss more often. Does not have to be combat related.
Traits are great for defining and customizing your character at a core level, and for roleplaying purposes.
Skill Tree
Each class should have skill trees that has MUTUALLY EXCLUSIVE options. For example, you can hack faster, or hack with a bonus to hacking skill. Or you get more damage mitigation from light armor OR you run faster in light armor. Mutually exclusive skill branch endings is something that has fallen out from RPGs for some weird ass reason. Mutually exclusive choices are great because you get more customization. Skill trees where you can "just grab everything" and which are linear is stupid imo. Like in Skyrim. Loved skyrim but DAMN the perks trees were bland and braindead. I'm hoping for skill trees that are not linear and where you have to make meaningful choices.
The worst case scenario for me are skill trees and a progression system that does not include mutually exclusive choices, that are linear, and where you can "obtain everything". The most fun thing about player builds, for gameplay and roleplaying, is having to make hard choices. What you get is a truly unique character.
A bad skill and progression system is one where your character can easily be the same as 2456 other characters.
Though I have put heavy weight on mutually exclusive choices above, I'm not talking about overdoing it either. Have branches and paths, with some mutually exclusive options. Make it advanced by some dual-mutually exclusive options giving a unique skill.
For example if I chose A over B and C over D, I can pick a skill that requires A+C, so I end up with A+C+AC and lose B+D+BD
Also Im heavily against free respecs. There should only be a few respecs in the game. One for free, then one at a heavy cost, then a third which will cause light permanent damage to your character, which increases for each respec after this.
I find it kinda retarded that you can go HEY YO IM A SOLO... nm lol Im a Netrunner now. Switching builds and skills "at will" DESTROYS your character's uniqueness. Though you shouldn't be penalized so hard you have to reroll. Hence 3-4 respecs at most.