Stop redefining MOTHERBOARD and #define AT90USB instead. Also put #ifndef AT90USB around the HardwareSerial_h trick, so now Printrboard / Brainwave support compiles on Arduino 1.0.2 as well.

Marlin/Marlin.h

 #ifndef MARLIN_H
 #define MARLIN_H
 
+#ifndef AT90USB
 #define  HardwareSerial_h // trick to disable the standard HWserial
+#endif
 
 #define  FORCE_INLINE __attribute__((always_inline)) inline
 
 
 #include "WString.h"
 
-#if MOTHERBOARD == 8  // Teensylu
+#ifdef AT90USB
   #define MYSERIAL Serial
 #else
   #define MYSERIAL MSerial

Marlin/MarlinSerial.cpp

 #include "Marlin.h"
 #include "MarlinSerial.h"
 
-#if MOTHERBOARD != 8 // !teensylu
+#ifndef AT90USB
 // this next line disables the entire HardwareSerial.cpp, 
 // this is so I can support Attiny series and any other chip without a uart
 #if defined(UBRRH) || defined(UBRR0H) || defined(UBRR1H) || defined(UBRR2H) || defined(UBRR3H)
 MarlinSerial MSerial;
 
 #endif // whole file
-#endif //teensylu
-
+#endif // !AT90USB

Marlin/MarlinSerial.h

 #define BYTE 0
 
 
-#if MOTHERBOARD != 8 // ! teensylu
+#ifndef AT90USB
 // Define constants and variables for buffering incoming serial data.  We're
 // using a ring buffer (I think), in which rx_buffer_head is the index of the
 // location to which to write the next incoming character and rx_buffer_tail
 };
 
 extern MarlinSerial MSerial;
-#endif // ! teensylu
+#endif // !AT90USB
 
 #endif

Marlin/pins.h

 * See http://reprap.org/wiki/Printrboard for more info
 ****************************************************************************************/
 #if MOTHERBOARD == 8 || MOTHERBOARD == 81
-#undef MOTHERBOARD
-#define MOTHERBOARD 8  // Disable MarlinSerial etc.
 #define KNOWN_BOARD 1
+#define AT90USB 1286  // Disable MarlinSerial etc.
 
 #ifndef __AVR_AT90USB1286__
 #error Oops!  Make sure you have 'Teensy++ 2.0' selected from the 'Tools -> Boards' menu.
    https://github.com/unrepentantgeek/brainwave-arduino
  ****************************************************************************************/
 #if MOTHERBOARD == 82
-#undef MOTHERBOARD
-#define MOTHERBOARD 8  // Disable MarlinSerial etc.
 #define KNOWN_BOARD 1
+#define AT90USB 646  // Disable MarlinSerial etc.
 
 #ifndef __AVR_AT90USB646__
 #error Oops!  Make sure you have 'Brainwave' selected from the 'Tools -> Boards' menu.

Marlin/stepper.cpp

 
     
     for(int8_t i=0; i < step_loops; i++) { // Take multiple steps per interrupt (For high speed moves) 
-      #if MOTHERBOARD != 8 // !teensylu
+      #ifndef AT90USB
       MSerial.checkRx(); // Check for serial chars.
-      #endif 
-      
+      #endif
+
       #ifdef ADVANCE
       counter_e += current_block->steps_e;
       if (counter_e > 0) {