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Biological taxonomy is lately being decided by the degree of relatedness between taxa. Visual appearance doesn't necessarily track relatedness, nor necessarily does current geographical distribution.
Last common ancestor does track relatedness; your cousin is such because of their last common ancestor with you, not how they look or where they were born.
Like Herpin Man said, the prior systems of taxonomy that depend on morphology have value to hobbyists. For that reason they are good to know but not to the exclusion of a more accurate taxonomy that is based on genetic relatedness (since for breeding purposes getting the species right is -- or should be, anyway -- pretty darned important).
After a quick read of the blog post, I don't see the "mess" -- looks like a pretty typical restructuring with relative clarity at the end of it. The fact that visually similar animals can be different species doesn't seem confusing to me (nor does the fact about other animals that have radically diverse appearances within one species) but I don't assume that speciation has anything really interesting to do with gross appearance, especially in a family that is very morphologically homogeneous to begin with.
I didn't see a link to the papers that made the changes, though; there's certainly much more to it than the blog post outlines.
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