Maintaining backwards compatibility with legacy kit is always a problem, if you want to move forward with new technology.
A decision was made to use SAM3X, which does not have EEPROM. I think the best solution is an i2c/spi EEPROM on the Due, could have been easily done , but wasn't. Storing data in Flash is a problem because downloading a sketch erases the Flash, storing data in 16u2 requires a hardware mod and/or new firmware in the 16u2.
As for software serial, I have been tempted to do a Due version, but with 4 real serial ports on the Due, is it necessary? It would mean time spent that could be spent on doing something possibly more useful. This is the same dilemma for Arduino, do they spend limited resources developing new stuff or spend time just to stay still?
It's a tradeoff, Paul has made the decision base on his needs, Arduino have made a different decision.