Wonders, like the terraformed terrain, will be a source of territory-wide bonuses, as you guessed. Resources are used in a more finite fashion now, and will be used for upgrading buildings or trading to AIs.
The reason that a lot of the bonuses have not been added back yet are twofold. First, I've been focused on other things and I'm tackling the more challenging and/or needs-most-testing stuff first. Secondly, with building services and some other things like that in the near future, I'm not really working on any sort of specific bonuses anywhere -- or at least I'm trying to avoid it. A lot of those bonuses will go to those sorts of services.