But if the results seem likely to be helpful in spite of flaws, ask that the problems be acknowledged, their likely biases assessed, and means for overcoming them in the future considered. Gives the impression of being written by an amateur without knowledge or training in the field. This looks to me like a high-quality undergraduate term paper, or something written for a popular magazine. Such comments are hurtful without being useful. Distinguish your objections from Your queries and suggestions.
Suggestions are simply alternatives for the author to consider.
The author needs to know what's essential to address. Since thomas kuhn published The Structure of Scientific Revolutions in 1962, it has been well known that all disciplines, even the physical sciences, are structured and divided by competing paradigms that cause serious problems of mutual incomprehension for their respective advocates. This phenomenon frequently puts the reviewer in a quandary. A reviewer might legitimately hold that an author's entire line of research is meaningless, since the author fails to address what the reviewer sees as the critical issues in the field, and reviewers cannot take the relativist's escape that everyone has his or her own approach. Many reviewers act as if they have privileged access to the truth.