feurig - It did seem to take a long time for the Arduino to evolve. However the Arduino team do seem to work hard and diligently to ensure there is smooth path forward for Arduino users.
I thought Dean Camera's Lightweight USB Framework for AVRs (LUFA - http://www.fourwalledcubicle.com/LUFA.php) showed how to replace the USB-to-serial. Paul Stoffregen's (pjrc.com) Teensy boards showed the advantages of doing it.
AFAIK, Paul Stoffregen's Teensy boards still have the sneakiest USB connection; they are HID devices, and can plug straight into most things.
FTDI, is not quite a "one trick pony". It is possible to do 'bit-banging' using some of the pins (I have never tried). So, in theory, it is possible to get it to talk to a different interface (IIRC, someone has used one to make an SPI programmer, and another to make a JTAG interface), or to set the boot pins and reset. Also, I think some are about $2.
I agree the ideal USB interface solution would be fully programable.
However, something low-cost, that avoids the need to install any drivers (on, at least, the main three platforms), and that does not create problems for users, for example by changing its USB class, would be better than where Maple is today.
Let's hope Maple 2 addresses the problems that users suffer.