I like your question. I don't have much of a concrete answer, but systems theory paired with queuing theory has been broadly useful for me in assessing situations and making back-of-the-napkin consequence estimations of various decisions.

Of course, I don't know of any book that teaches systems theory "as a technology" -- it's something I've learned by reading a lot of books on different things and picking up the threads they have in common.

Systems theory relies, really, on a complete map of the causal network of a situation. We're not at a point where we can give a step-by-step instruction for inferring the causal network behind situations. We have some ideas on how to statistically do this in a limited fashion (see Judea Perl) but the general problem is still one of creativity, intuition, fact-checking, Bayesian probability, and so on. You get good at it by doing it a lot in various situations and reflecting on your performance -- the way you get good at most mental skills.

I may have ended up answering a different question to the one you asked, but these were my thoughts.

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I guess with all my rambling I'm trying to say that ultimately, "better thinking" boils down to "a more complete understanding of situations" and the best way to get there in my experience has been the scientific method, democracy (in the true sense of the word), and curiosity. These are very complex technologies that are not easy to teach.