E compares vehicles powered by natural gas with those burning gasoline or diesel fuel, with those parallels with vehicles (both in plural form), powered parallels with burning (both participle), and natural gas parallels with gasoline and diesel fuel (both noun). E is clear and concise. With the addition of “do”, E would further clarify the subject for the second term in this comparison, however adding do is optional. To compare certain pollutant with those burning gasoline or diesel fuel, E would have to read, “less of certain pollutants than of burning of gasoline or diesel fuel”.
In B, fewer of sth. is unidiomatic when it speaks to quantity. The correct wording should be fewer certain pollutants. less of in E speaks to volume, which is uncountable. Furthermore, B compare vehicles, a noun, with burning gasoline or diesel fuel, an action, mismatching the subjects of the comparison.
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