Fastest communication between Arduino and PC
Switch to using SerialUSB instead and use the other USB port. The baud rate is meaningless then - it runs at the speed of the USB port, which is a lot faster than serial (Linux reports it as 480Mbps, though I can't see an 84MHz chip doing that...).

void setup() {
    SerialUSB.begin(115200); // The number is irrelevant but it needs something in there
}

void loop() {
    SerialUSB.println(millis());
    delay(100);
}


For greater throughput you could devise some packet-based binary protocol to optimize your data flow to use less bytes.