ADC / data acquisition board - general layout question
1) Initially routing diagram 2 is the better of the two. 

2) It is always best to avoid running digital lines (or their ground returns) close to or over ADC lines, even if they are considered constant or slow. There can often be moderate levels of digital noise even on stable digital lines.

3) Consider moving the IO-expander right up against the MCU to reduce high speed trace lengths. 

Widening the cutout lines between the two ground planes would better isolate the digital and analog signals and reduce potential noise transfer. 

If the digital supply is a switcher type consider moving it further away from the analog supply components.

You might even try to keep the analog ground separated all the way back to the main power entry point or the filter components of the analog supply. Connect the two grounds at only one point.

To minimize radiated emissions reduce the length and loop size of all high speed signals, minimize the number of sharp angles in traces with high speed signals.

Keeping the analog input lines short and direct can help reduce noise. However this might be a compromise if the ADC uses a serial interface (with longer high speed lines).

4) No.