While I am admittedly a little too lazy to do the math, it seems to me that researching increased mining speed is really not worth it. Because there is only so much crystal and metal per mine, I end up having less crystal to mine by spending crystal researching how to improve the speed at which it is mined. Unless I have been focusing on mining research alone (which is probably a bad idea), by the time I can spend the resources to research the most advanced levels of mining, the mines will not have a lot left in them, making the research expenditure a waste. This is especially so when I spend so much resources for a mere 3% increase.
Suggestion: If this research improved the rate by which I obtained resources via refinery freighters as well then the research might then be worth investing in. -Perhaps mining research already does affect the efficiency of get resources via freighters, but I have not noticed.