I am not too sure why, but probably the technology in St. Petersburg was vastly improved in the early 1800s, probably with the aid of new minting equipments from the UK. Remember that St. Petersburg was still the capital city of Russia at this time.
With that in mind, while Ekaterinburg severely lagged behind in her copper coinages and eventually letting St. Petersburg to handle all of the coinages, this soon spelt trouble for only allowing one mint to deal with the whole nation's coinage. As WWI sets in, and St. Petersburg's men were conscripted into WWI, this spelt enough trouble for future coinages.
The previous St. Petersburg mint was rumored to be damaged during the First World War, and there was no official coinages from 1918-1920. The capital city was then moved to Moscow under Lenin. Goznak mint, based in Moscow was then setup in 1919 to compensate the loss of St. Petersburg mint, but it was never in full use until 1942.
And that was the brief history of the two mints. However if we are to compare what both mints currently mint, it seems that Moscow mint handles most of the gold and more Ni-Cupro coinages, where St. Petersburg handles most of the palladium and platinum coinages. Both mints seem to share the job in minting silver coinages. I am not too sure why, but there might be an agreement on what mint strikes what particular type of coinages.
What is more interesting is the difference of finishes both mints deploy. If you are to take a look at the common bimetal 10 ruble coins produced by both mints, it seems that St. Petersburg has a more refined finished look whereas Moscow mint seems to be much cruder, possibly because Moscow mint does not have the same technology as St. Petersburg (but why???
