While I would agree with you that the submission of a further paper would be the correct (and usual) course of action if one wanted to publicise an alternative theory, the most obvious problem here is one of time-delay. It is not unusual for there to be an interval of a year between the submission of a paper to the JBAA and its publication, by which time most readers will have forgotten what the original paper was about anyway! I can’t say whether this is typical of other learned Journals, but even in their case the adoption of “pre-publication” revelation has proved a necessary part of the review process – the “arXiv” server being the prime example. While a delay of this magnitude might be acceptable for theories involving fundamental issues, I do think a faster process is needed for the sort of papers published in the JBAA. Bi-monthly Letters are certainly not perfect in this respect, but they are definitely better than annual papers!
The above of course assumes that one wishes to put forward an alternative theory, rather than simply comment on certain aspects of the original paper (as I was). These comments may not invalidate the original conclusions, but need to be addressed before a fully-robust position can be reached. In this case, a formal paper is almost certainly inappropriate and so the responder needs a means of putting his or her ideas forward in a different way. Currently, the Letters section is the only vehicle available for this and so it must be made clear whether such submissions are (or are not) acceptable as Letters – and if they are not, how they are to be published must also be made clear.
Discussion via the BAA Forum can, as you say, help to clarify ideas (assuming this is required). However, it suffers not only from the problems alluded to in my previous post, but (like any forum) can also result in “off-topic” comments and somewhat random trains of thought. It will also only reach those who are dedicated “Forum watchers” whereas a published comment will place itself before the eyes of the entire membership – few may read it, but at least it will clearly announce its presence. Furthermore, even if the Forum reaches a consensus conclusion on the ideas being put forward, how is this to be reflected back into the JBAA as a counter to the original article? Presumably as a Letter, at which point the discussion might well start all over again!