I am working on my masters thesis which is the first time that I have ever really taken part in research activities. Throughout the experience I have learned a lot and I think that I would like to pursue a PhD in the field that I am currently working in right now. However, I feel that when all is said and done with my masters thesis, the end product will not be that great. There are a number of factors that I think contribute to this - the first being that it's my first time doing original research and second I am the first student of my supervisor, so we are experiencing the student-supervisor relationship both for the first time. But given that, I think it is primarily a function of my introduction to research. A similar analogy would be a first year undergraduate student that doesn't do well, but finds their groove in the last couple years of the program.
My concern, however, is that if I produce a low quality thesis that I might actually be disadvantaged compared to a recently graduated undergraduate student. For example, my undergrad/grad GPA's were (3.5/3.8) and assume that the undergraduate also had a GPA of 3.5-3.8, but I can foresee that a committee might view my weak thesis as an inability to do research in contrast to the undergraduate does not have any published research either, but doesn't show signs of being a "weak researcher" by nature of not having done any.
So the question really becomes whether or not somebodies MSc experience is a good predictor of how they would fair out as a PhD student, and whether somebody applying to a program with an MSc can actually be disadvantaged.
Edit: Perhaps mentioning my perspective on the MSc experience in my SOP might be of benefit? Unless, all of this might be moot if entrance committees might not even read your MSc thesis.