Scenario one: Thanos has consistently been portrayed as a genius. He is going to take note that the JLA is a team, and also that several of the team members have a home city where they fight crime solo. He is going to arrange for distractions and then try to pick off the Gems one by one. If his throne is considered standard equipment, Thanos will probably go after the Gems in the order listed in scenario two. Once he has the Time Gem, it should be relatively easy to pick off the other Gems.