Personally I would like to have a mixed learn by doing and action skills system that doesn't involve perks at all. This would involve changing other core gameplay systems as well.
Why no perks? I just don't think they fit in a survival game. They feel too "Gamey". Levelling up you character to choose what to magically be better at doesn't make me feel immersed in my character.
So what do I think works?
I think A15 when I started was the closest to solid but it was still tied to perks. I'd suggest:
1) Return item quality 1-600 (This fleshed out the progression journey of your character)
2) Bring back degradation (This keeps your character always needing to be out in the world looting. It just needs to be balanced so it isn't tedious)
2) Bring back schematics as the only way to unlock new recipes to unlock for craftable items (Makes every play through unique, adding to replayability. For example, you might find a sniper rifle schematic on day 1 or it might be day 50. These are looted in the world, rewarded for quests and sold by traders.)
3) Complete RNG loot like it was in previous alphas where you could find a really good item on day one but the chance was low (Again, makes each playthrough unique, adding to replayability)
4) To improve item quality, a mixture of crafting, scrapping and reading corresponding magazines would get you to quality 500. This diversifies the quality improvement system to make it less repetitive.
5) All actions in the world improve character stats like they did in A15/A16.
6) Item quality 501-600 can only be looted in the world, maybe quest rewards also. (Encourages players to keep active out in the world)
For me, this would be perfect. The systems are intuitive and already proven to work.
