The phrase "root of the trouble" can be replaced with a variety of synonyms depending on the context of the situation. For instance, it could be described as the "underlying cause", "source of the problem" or "origin of the issue". Alternatively, one could say that it is the "fundamental difficulty", "central dilemma", or "core complication". In some cases, it may be referred to as the "crux of the matter", "heart of the conflict" or "essence of the challenge". Ultimately, there are many ways to express the idea of the "root of the trouble" and choosing the right synonym is essential to effectively communicate the issue at hand.