What is a faster alternative to parseInt()?
The annoying thing about parseInt() is not its speed, it's the fact
that it relies on a timeout. If the timeout is too long, it slows you
down. If it's too short, it may induce errors.

A safer way to parse the sort of messages you are using is to buffer all
the incoming characters until you find a carriage return, then parse the
whole line. For example:

// Just echo the messages with a different separator.
void parse(char *buffer)
{
    char *s = strtok(buffer, ",");
    int x = atoi(s);
    s = strtok(NULL, ",");
    int y = atoi(s);
    Serial.print(x);
    Serial.print(':');
    Serial.println(y);
}

void loop()
{
    static char buffer[BUFFER_SZ];
    static size_t lg = 0;
    while (Serial.available()) {
        char c = Serial.read();
        if (c == '\r') {        // carriage return
            buffer[lg] = '\0';  // terminate the string
            parse(buffer);
            lg = 0;             // get ready for next message
        }
        else if (lg &lt; BUFFER_SZ - 1) {
            buffer[lg++] = c;
        }
    }
}


Note that you should add some error checking when you call strtok().