The total current of the device travels through these pins and the tiny bond wires inside. Having many pins reduces the impedance (AC and DC) of the power supply coming into the chip and allows the part to work well under high impulsive transient loading (typical of fast digital circuits) and reduce noise and other issues. read more
This is the signal integrity part. In the BGA pinout figure below, the red, purple, dark navy and yellow pins are power pins (many of them at different voltages), and the green pins are ground. To reduce inductance, you want to place power VSS and VCC pins together. So if you see ground pins that are not next to one of the power pins, they are almost certain for signal integrity. read more
The FPGA can draw up to 30 or 40 amps at 1.2 volts. The high number of pins is required to provide a low impedance path for the high current supply to the programmable logic array. The Vccaux pins supply power to some supporting circuitry, including the JTAG interface. The pattern of Vcco and ground pins supply power to the I/O banks. read more