The problem with what you're saying (that grammars are not necessarily the best representations of complex hierarchical structures, with which I agree) is that anything that can represent a complex hierarchical structure as well as a grammar must necessarily be equivalent in computational power to that grammar- and unfortunately, we know of no computational process that cannot be expressed as a grammar at least in principle.
"Unfortunately" because this means that any representation of such a process you may want to pick over a gramar, that is not a grammar, will either have to be reducible to a grammar, or fail to capture the expressive power of the modelled process.
So, sure, a "tree" may not be the best way to model natural language. But we don't have the theoretical tools to figure out what can be a better representation than that.
"Unfortunately" because this means that any representation of such a process you may want to pick over a gramar, that is not a grammar, will either have to be reducible to a grammar, or fail to capture the expressive power of the modelled process.
So, sure, a "tree" may not be the best way to model natural language. But we don't have the theoretical tools to figure out what can be a better representation than that.