As it is well known, in addition to novel aspects, every study has limitations, since it is impossible to collect fully representative samples, to address every factor and to include every possible control. Research limitations cannot be ignored, otherwise, referees will insist that they are emphasized. However,if the limitations are highlighted too strongly the paper(thesis) may be rejected In one sense, the degree to which you can afford to describe the limitations varies inversely with the degree of limitations. In other words, if your study was extremely comprehensive, covering a very large range of potential factors with intensive and extensive sampling (and hence there were very small standard errors), the limitations could be discussed in great detail without worrying that this may lead to rejection of the paper. In contrast, if the limitations are severe (e.g., if you took very few samples or monitored just a few of a large class of pollutants at a few sites), they have to be mentioned carefully, and in such cases a strategy for addressing the limitations is required.
Usually, the best way to deal with severe limitations is to justify them in the Introduction, for example, by clearly stating why a few populations were selected for study or you focusedon a few compounds (rather than limited the study to them).
Generally, there is then no need to provide further justification of the limitations, provided that you do not make unwarranted extrapolations in the Discussion.
This strategy may be very useful for further grant applications, since if the paper is accepted, you can state that the potential validity of your hypothesis (that the findings might be generally applicable) has been accepted, because if referees do not object to the statement they are implicitly acknowledging the possibility. Hence, it may facilitate the publication of two or more papers rather than just one.
The importance of treating novelty and limitations carefully, in all sections of a paper, can be illustrated by a paper describing a process detected in Boreal forest ecosystems, which was submitted to Nature. A major problem was that the authors initially mentioned, repeatedly, that although the process they investigated had not been previously detected in natural environments, it had been shown to occur in laboratory settings, virtually asking the referees to reject the paper since the study was merely confirmatory. The paper was subsequently revised, before submission, by stressing when this was first mentioned that conditions were unrealistic in the previous laboratory experiments (concentrations of substrates were much higher than would ever be found in the field) and simply mentioning at other points that this was the first report of its occurrence in any ecosystem. These simple changes highlighted the novelty of the study, without completely ignoring its limitations, and the paper was accepted.
Blackwell, J., & Martin, J. (2011). A scientific approach to scientific writing (pp.16-17). Springer Science & Business Media.