Without guilds/corporations to provide a benefit to having multiple copies of a resource type, we need to be sure that the resource has plot-benefits when used "as intended". This helps the AI as well as justifying the resources existance. Trade for other resources is one thing, but I don't think it adds up enough in a typical game to justify multiple copies.
If a Banana farm is just all-round better than a banana plantation, that is not so good. (I need to check, is the coin the same?) The various options ought to produce results which are comparable, especially if they produce interesting choices (do I pick the more-food option or the more-money, resource-to-trade option?)
Of course it might be nice if there was some global, gentle corporation-like effect. So if a civ has more than one of *any* type of resource they get +1 gold per extra, or a trade route % boost or similar in *all* cities. If you have tons of bananas, economies of scale come in and your empire benefits. This avoids serious imbalances I think, and means that second Marble has some benefit even it it isn't immediately obvious, and it is not directly comparable with building a mine or farm in the plot instead (sure I get extra X or Y or Z in the city, but the empire overall doesn't get the N gold per turn creating the intended resource-gatherer would)