My instinct, having done no research on the topic, suggests that Rash"i is in fact softening both ends of the descriptive spectrum to make the point that "there are no X people, just X questions".
Note that the wise son is not the only one whose designation shifts between the text of the Y'rushalmi to Rash"i's expression of it. Tipesh (stupid) also becomes sho'el derech s'tuma (asks [a] general [question]).
"תני ר' חייה "כנגד ארבעה בנים דיברה תורה: בן חכם, בן רשע, בן טיפש, בן שאינו יודע לשאול
With the exception of the wicked son, whose motivation in initiating the dialogue is assumed to be misfounded due to his religious or philosophical shortcomings, the sons could each be the personification of a mode of questioning rather than a human typology. Similarly, the response to each of them is a response to the approach he is taking rather than a wholesale reaction to what he represents. (Again, the wicked one is the exception to this rule.)
It therefore would follow logically that they are categorized by the interrogative stance they demonstrate (Rash"i's version) and not the their underlying inferred intellectual personalities (Y'rushalmi's version).