My advice is to identify what the challenges or requirements are and then explain how B meets them (and other methods do not). I encourage you to focus on the positive -- what you are able to achieve -- rather than the negative -- the ways that other people have failed. Also, in many cases I find it is helpful to first list the requirements or goals or challenges, then explain how your approach meets those requirements or goals or addresses those challenges.
Bad: "We use method B."
- This is bad, because there is no explanation of why you have selected B.
Bad: "We use method B, because method A is flawed."
- This is bad, because it does not explain concretely why B is better than A.
Better, but not ideal: "We use method B, because method A has problems P, Q, R."
- This is better, because this provides some explanation of why you selected method B and specifically what the advantages are, but not ideal, because it is focused on tearing down someone else's work, rather than on what you're trying to achieve.
Best: "Ideally, we would like an evaluation method that has properties X, Y, Z. We ultimately chose to use method B, because it provides all three properties. Others have used method A, which provides property X but does not provide property Y, Z. In our setting Z is particularly important."
In my opinion, this is best, because it is focused on the positive - what you are trying to accomplish and what you have achieved; and does so in a way that explains why you chose the method you did, while treating prior work with respect.
If there are multiple options for evaluation methodology, you might even consider a table where you compare all the options: you can have one row per candidate method, one column per requirement or desirable property, and checkboxes in the cells indicating which methods meet which requirements. This can provide a visual summary that makes it easy to quickly understand why you have chosen your particular method. You should probably supplement it with a detailed definition of each property and discussion of why each property is relevant and important.
If some of the explanation gets too detailed or lengthy and is distracting, one option is to put that detailed explanation in an appendix, and summarize the main idea in the body of the paper with a reference to the appendix for further elaboration.