what are some examples of how evolution's limitations prevented species from climbing to the absolute highest peak on the fitness scale?
The "limitations" of evolution is somewhat subjective, I suppose, but a couple of the important ones include random mutations, lack of foresight, and environment. Evolution is a complex process by which mutations occur which either benefit an organism, making it more fit, harming the organism, leading (usually) to death, or to no noticeable change. Over time, these mutations bring about significant phenotypic changes. There's no goal, no purpose to it. In your example of plants, chlorophyll could certainly have evolved a structure that absorbed light in different wavelengths. 

Another example is the difference between the vertebrate eye vs the octopus eye. For mammalian eyes, the optic nerve covers part of the retina. This is commonly known as the "Blind spot". For Cephalopods, on the other hand, the optic nerve is located behind the retina, so they have no bind spot. 

Both of these examples are the result of random mutations coinciding with ideal (or non-ideal) environmental situations. The author of the post you cited is accurate to say that evolution is not an engineer, working towards a goal. The only goal of evolution is "What maintains life?" It's merely millennia of trial and error, and occasionally calamities occur, causing extinctions and loss of genetic potential.

I really think ANY characteristic of any species you care to name could be considered a result of evolution's limitations.