Actually, the way I learned it, there were two standard systems- cgs for "centimeter- gram- second" and mks for "meter- kilogram- second". If you are working with "normal" sizes then mks is natural- a gram is awfully small (about the mass of a raisin!). That's why there are often two names for particular measurements: in mks, the unit of force is the Newton (which will accelerate a mass of one kilogram at one meter per second per second) and the unit of energy is the Joule (the work done in applying a one Newton force for a distance of one meter); in cgs, the dyne (which will accelerate a mass of one gram at one centimeter per second per second-and is really small weak) and the erg (the work done in applying a one dyne force for a distance of one centimeter- now that's almost non-existant!).
It's the fact that most measurements are in the mks range rather than the cgs range that make mks (and therefore the kilogram) the standard.
Maybe it was just a case of one standards decision following after another. The original "gram" was handy because a cubic centimeter of liquid water near the ice point weighs about that much. The "cgs" system was quite suitable for ordinary chemistry experiments; it grew more unwieldy when considering larger things (industrial and astronomical). Maybe they should have invented another name, for example, a "pond" for 1,000 grams and proposed a "mps" system. But gram was already established, much data recorded in that unit (and multiples like km) and conversion was an easy slide of decimal point three digits leftward. So, "mks" it became.
P.S. I have in mind that "pond" would mean a unit of "ponderable" mass.
P.S. Units for electromagnetism also complicate the story.