3.3V logic has become new standard. 5V devices will probably go off the sale somewhere in the far future (I believe because higher electricity consumption). I have found an easy solution for comunicating DUE with 5V RS485 transcievers in this document: How to interface a 5V Transceiver to a 3V Controller
And I would love to see an option on all Arduino boards (Except those that allready run on 3.3V), to have VCC running 3.3V or 5V, depending on a user choise. There are guides on the web how to convert Arduino (at least Leonardo which I am using) from 5V VCC to 3.3V. MCUs runns on 3.3V flawlessly, only downside is that MCU are not able to run with higher clocks at low VCC voltage (For Leonardo, 5V is on 16MHz but 3.3V can run only at 8MHz).