Its the transfer rate per link (or lane) that changed within the standard.
v1 had 250MB/s
v2 doubled that to 500MB/s
v2.1 reduced the overhead due to management/control, giving more room for data.
v3 will double the rate again to 1000MB/s per link
This is just the squirting of data to and from the graphics card, its the construction of the cards that make the real differences in speed.