The "best method" I have tried is to have teams. Each player moves once each turn. This (of course) only works well if there is an even number of players however. The only other method I liked with an odd number of players is a random draw and that sometimes will not work out too well for a player. I had a player suggest one figure per player and make them all characters... and push the RPG flavor...that could work as well, but it can end, real quick that way.
IMO, Strange Aeons is a great game but if you keep it simple (by not adding too much) and keep it with just two players, it is a simply
FANTASTIC game. ( <-- note: tenticle green! )
For my convention, I am using pre-built scenarios, so it is not nearly as much of an issue as I can balance the forces in such a way that if I have 1 player sign up ....no problem, they play me. 2...no problem...3/5 is my only issue so I blance my forces to be both "even" and with an adjustment be able to handle differing number of players.