There are three main approaches in doing a Lean-Agile Transformation.
We rarely take the first one because it is a one-size-fits all approach. The second has people re-invent the wheel and is, unfortunately undertaken by people without deep experience. FLEX takes the later approach.
The question remains, however, what solutions do you start with? There are two main approaches to this:
Taking low hanging-fruit (that is, easy changes with big improvements) is that it does not account for its effect on later changes. Sometimes starting with the wrong thing may be easy but may make later changes more difficult. For example, starting with Scrum may achieve better Scrum teams but 1) doesn’t necessarily help the bigger picture problems and 2) may make it that teams don’t want to slow down later when they need to in order to work with other teams. That is, teaching local optimization as a start can make it harder to achieve value stream optimization. See Successful Pilots Can Hurt an Agile Organization.
When considering what to do first (or next) one must consider the overall benefit and/or cost over time. Another example is starting with Test-Driven Development when teams can’t really break down stories or do refactoring at the time they learn it. This may have them decide TDD isn’t very useful when it is.