Designing system for multiple SPI and I2C slaves
You have covered the 'electrical' and 'finished state' issues pretty well.

However, think of the process of building, debugging and testing the system.

The potential advantages of SEPARATE seem to be quite compelling:


Any electrical problems or bugs should only effect one device
Software for each slave device should be independent, so testing
parts of the incomplete system should be easier because of this
The devices might need slightly different I2C (and maybe SPI) setups.
For example, the data and clock may be in different phases, or worse,
may use the same I2C address.
Finally, it would be relatively easy to combine slaves on a common
peripheral, once everything is working, but getting the whole system
working will be harder on shared peripheral interfaces.