I don't see any i2c pullups on the board. Are you complaining that the library enables them in the chip? That should be easy enough to change (but why?)
The 50-60 dPins and 12 Apins of a Due (like on a mega) plus 2x i2c + 4x UART plus the RAM and the cpu power are of invaluable advantage.
Teensy is in development with a 180 MHz Cortex-M4F chip. A more powerful ESP chip is also coming. These 3 are probably the near-term future for people wanting more powerful Arduino-compatible boards.
is it already available?
But back to topic:The Due is highly neglected currently IMO,
perhaps they'll leverage the already-developed STM32 core library or older stuff from Maple?
Some CPU's are 5v tolerant even though they run on 3.3v normally.......I look forward especially to the 12 bit ADC and also the 12 bit DAC, which dosent come on any other boards.