5V shield only ruins your day if you power it from 5V.
So power it from 3.3V instead and all is honky-dory.
Gives me an idea for a DUE shield. Bring all pins in, but only 3.3V for power. Any device must be 3.3V device.
2nd shield - Bring 5V in, but provide offset female headers that are all 3.3/5V buffered with TXB0108 chips or equivalent. Fully compatible with 5V shields, but only 3.3V is exchanged with the DUE.