Personally, I quite like this mechanic but I don't feel like it has reached its full potential yet. The way I see it, there should be three options:
1) Harvest, removing the resource from the map and adding it to your empire's resource pool
2) Cultivation, adding food, production or commerce yields to those tiles (build a farm, mine, camp or plantation)
3) Preservation, leaving the resource alone in return for non-vital yields (culture, science, faith, tourism and appeal) by building a national park or a preserve or an observation post.
This would apply to all resources,
e.g. 1: harvesting wheat, should allow that city to build a "brewery", which provides the "beer" luxury resource, which you can trade, while cultivating the wheat by building a farm on top provides an extra +1 food bonus to that city and preserving the wheat by building a park on top of it, increases its appeal and add +1 culture.
Similarly, you can choose to hunt exotic animals on the map for Furs luxuries, build a camp/pasture to domesticate and sell them in your cities (provides +gold on that tile ), or build a preserve where you study the animals, providing science.
Or for instance, when it comes to Iron ore: Do you completely excavate it, so you can build units with it, do you build a mine for extra tool production in the city (= extra production yield) or do you leave the ore alone for extra appeal and the ability to attract extra tourists to these beautiful reddish hills?
Preservation and Cultivation can be made more appealing by founding a pantheon which improves yields of either tile improvements or the flat resource itself. (the usefulness of harvesting seems obvious if that's the only way to obtain and trade resources)
This can also be tied to hidden agenda's (Ecologist could be a valid HA, aka someone who HATES people who harvest or cultivate their civ's natural resources)
AS for the mechanic as it is right now... Harvesting seems occasionally interesting, if you need the food in a pinch, but i feel like it's almost always better to not do so, as the extra tile yields will have a higher longterm benefit.
Finally, slightly OT but... I feel like chopping rainforests and removing marshes should yield food and gold respectively, especially as chopping forests already provides production, so...
