Resources, economy, crafting and perk system
With a very urban setting I suppose hunting should be the less obvious source of income. But if collecting pelts is once again to be a feature(hunting can be really nice), it would be great if there wasn't a maximum ammount for each pelt type that you can carry- but one big storage like from FC3&4, for all collectable loot.
As for generating cash, unlocking weaponry etc, it would be nice if the black market from FC2 returned with these missions to intercept[regime] convoys/transport choppers etc- that best bring weapons from abroad. Since the regime apparently has an iron grasp of the people, earning weapons from smuggling networks should be extremely expensive(with the upside you get to make specific orders). Money rewards for each successful convoy/armory heist is guaranteed(can be a two-stage mission), with a chance of getting a special weapon ordered by one of Castillo's generals- sometimes by having to kill the general and his guard.
Crafting is pretty good as it is really, has evolved through five games after all.
As for experience points and perks- I think I'd prefer the system from FC3&4. Getting stuck on having to use weapons/tricks I like less to get those sweet perk points is a little tedious sometimes.