This has always bothered me.

"Flipped" is perhaps not completely accurate. A kilo-something is always 1000 something, and so doesn't say so much. What is counter-intuitive and bothers me is kg is the basic SI unit for mass (rather than g), so that other SI units (eg. Joule) are defined in terms of kilograms, not grams. 

Thus eg. 1 J = 1 (kg m^(2))/s^(2)

I guess it is for convenience - it makes other units have more practically useful magnitudes.