When trying to consider a decision or idea thoroughly, there are several synonyms to use instead of "thinking over" or "thinking through." One alternative phrase could be "pondering deeply," which suggests a more profound level of thought and reflection. "Analyzing thoroughly" is another option, which emphasizes breaking down all aspects of an issue. "Reflecting on" implies a more personal, introspective approach to considering a matter. "Deliberating carefully" suggests a more intentional, purposeful process of deciding. Finally, "mulling over" is a more informal option, but still conveys the idea of taking time to consider something thoughtfully and deeply.