To me the real problem is the Due has lots of attractive features but many of them are disabled by the board. You can't use the real-time clock properly, the DAC would be 100 times more useful with a 0-5V amplifier, the ethernet pins are inaccessible, I2C has silly pullups (but only on one).
Some different design choices might have pushed the Due in a different direction. The Teensy is much more useful for a bigger range of things, although it's hampered by its desire to be small, so some useful pins are more difficult to access. It also has better library support for USB type things which the Due would also be good at.
I can't see the Due going away. It may not be stocked at Mouser next year but I'm sure you will be able to buy new ones at reasonable prices 10 years from now.