Finding an affordable integrated USB MCU
Microchip has some nice 8-bit microcontrollers with USB capabilities and internal oscillator.

The cheapest one would be PIC16F1455:


  Cheap in small-medium quantities (~100).


The PIC16F1455 is available from Digikey at $1.30 in quantities of 100.


  Native high-speed USB interface.


Universal Serial Bus 2.0 Module with clock recovery from USB host. Supports low-speed (1.5 Mbit/s) &amp; full-speed (12 Mbit/s).


  Ideally, no external crystal required for USB operation


Internal 48 MHz Oscillator


  Ideally, available in a hand-solderable package. Definitely not BGA,
  preferably not QFN


Available in PDIP package.


  Two U(S)ARTs, one capable of being used for SWD, one as a regular UART
  for user defined communication with the main MCU


Has only one USART module, but also has an SPI/I2C module.

Toolchain:


Microchip MPLAB X: free IDE, based on Netbeans, works on Windows, Mac OS, Linux
Microchip XC8 compiler: free with no optimization, works on Windows, Mac OS, Linux