Is it preferable to list the limitations of the presented method in the paper?
Actually, in every field, limitations should be mentioned. Otherwise the paper gives an incomplete account of what is known and what is not.
But that assumes that the author(s) recognize the limitations and that may not be an easy thing to do in some fields. In some situations, however, the limitations may be obvious to the reader, and thus are omitted. Some limitations might be trivial, though I'm having trouble coming up with a quick example of that. And, in statistical studies, the limitations are well known from the methodology used; sample size and such.
But including limitations should not negatively affect the likelihood of acceptance. Quite the opposite, I think. A reviewer, noticing an unstated, but important, limitation would be likely to comment on it and suggest an update.