Added bi-directional 3v3 to 5v converter using popular BSS138 mosfets. Added a voltage divider on ADC, so that is also 5V tolerant. The accuracy of ADC measurements will depend on the resistor accuracy, it can be taken care of in software using a calibration routine.
There is a lot of real estate on the board, its logical to add in a usb -usart chip. I'd use CP2102, as I use it for all my projects and its a excellent option. Its running in one of my project since 2 years which is powered 24x7.
I'm still not settled on the power supply section, I've thrown in a 1117 to get 3v3. Ideal solution would be to use a switching regulator, so it can be used with battery powered applications.
I think I'll have to make a trade off between choosing the USB-usart chip and a switching regulator.