Pascal, farad, joule aren't base units, they are derived units.

Ideally, the base units should be prefixless. Except for kilogram, they all are.

Imagine a system exactly the same as SI, except instead of the kilogram, it had the kram, where 1 kram = 1 kilogram... then the gram would be the millikram, the milligram would become microkram, the microgram would become the nanokram, etc... if you were starting from scratch, without any historical baggage, wouldn't such a system be superior? But of course, we aren't starting without historical baggage – almost everybody knows what a kilogram is, kram is a word I just now made up.

I think some derived units being "poorly proportioned" is inevitable given the physics we have.

If the base unit were gram, megapascals would be gigapascals, microfarads would be nanofarads, and megajoules gigajoules. Similarly a watt would be what's now a milliwatt and most "everyday" powers (except in electronics) would be kilowatts or megawatts.