When designing a shower with 2 shower heads is it best to have the heads on opposite walls(facing each other) or adjacent walls (where water will come at a 90 degree angle)?

The location of the shower head is simply a matter of taste. I would consider however that when installing them that they can be turned off and on by themselves through valves installed. Otherwise if you have them on both ends you would not be able to walk out of the water spray.
To determine what would work for you would depend on how big the shower is, what type of spray head, If you want both high or one high and one lower. The big advantage of installing a custom shower is you get what YOU want. Be creative.

The house we recently moved into has 7 shower heads in the master suite. The main one is the traditional type coming out of the front wall, and alongside that is a hand held massaging type. There are two body jets (about 3" diameter head) also on the front wall, and two on the back wall. Then there is a large unit on the ceiling that acts as a rainfall effect. They are all controlled by a diverter valve. I highly recommend a valve of some sort that allows you to turn them on/off. 99% of the time, only the main head is turned on at my house.