Nature has already perfected coffee, just as nature has already perfected ALL of the foods we eat. No amount of genetic engineering can make food taste better than hundreds of thousands of years of co-evolution (between plant and animal). The notion is absurd. And no, selective breeding is NOT the same thing as genetic engineering.
Um, evolution in most plants is "trying to make them taste BAD", otherwise, they... get eaten.
Nature's evolutionary "perfection", as a human might define it, would be a plant that replaces every living thing on the planet.
Of course, in reality evolution has no "goal". It is not "trying" anything. Producing something that is more fit is no more a "goal" of evolution than having a boulder roll downhill is a "goal" of gravity. Evolution is the simple outcome of the mathematics of self-replicating systems.