What's the best way to justify your choice of baseline methods for academic paper?
When you propose a method in a research paper, it is customary to describe how you came up with the method and why choose it over the others available in literature. There are a few tips you could follow to justify your selection.


The traditional way to do this is by doing a thorough literature survey of all other methods assessing the advantages and shortcoming of each and then show how your chosen method could probably supersede those methods.
Sometimes you may find many such methods that are applicable but for which you cannot find existing results. In such a case, the best thing to do is to produce results for all of those methods and select the one with least drawbacks and most desirable merits. If the amount of publishable work exceeds your paper limit (or if your time is limited), choose one among such methods for your current publication, but discuss the other methods that can also be applied that could be of scope for future work for research. 
A few journal publishers would also welcome negative results (such as PLoS ONE). Hence you could assess a method and show how suitable/unsuitable it is for a certain application based on the results.