Gen 2x1 uses a slightly more efficient error correction method than 1x2, so even though the number of bits going over the line is the same, the effective data transfer rate is higher.

Meanwhile, Gen 1x2 uses half the bandwidth that 2x1 requires, which makes the design of the chips, PCBs, and cables a lot easier. If a Gen 2x1 link fails to operate reliably, it will actually downgrade to 1x2 if possible.