In order to make a useful site, it is good to keep the different categories of questions well threaded by subject matter. A good guide is to start with the arxiv categories, so that a question comes with an arxiv category, and you can browse the questions in only one category.
If the question is about an existing paper, you can link to the paper and to the arxiv category, and then it will be automatic. But you can also sub-thread spin-off questions in a tree structure.
I think this is important, because the lack of question-threading on stackexchange means it only works for a short while before the content becomes unmanagable. Flat lists can't work once there are too many questions.
In order to do this, you need to have a different "category" system than a flat list, with categories including sub-categories, they are directories really, and each question sits in a given directory, so it belongs to one main category, but it has soft-links to other categories, so that it can appear in other sections, just as in arxiv. This requires only a little programming to implement, but I think it is critical, if the site is to be capable of unlimited growth.
(I am willing to manually classify all the questions to date by arxiv category, and by subthread, to start off the classification, it is a thankless job, but it doesn't take long, so long as you have a directory structure of the categories, with arxiv sections the main categories, and access to the questions)