Times vary a lot between journals and, I believe, disciplines. Two months seems like a relatively long period to me but not unheard of. Out of your three reasons I would not opt for 2 or three depending, of course on the form for submitting manuscripts. If it is digital I am sure 2 and 3 would not be high on the list, if it is manual, by post or e-mail, then the likelihood is higher.
I think a busy editor is one possibility. It is not clear from your question if this is "with the editor" after submission or "with the editor" after review. If we consider the former, the most likely reason, in my experience, is that it has proven hard for the editor to get reviewers to accept to review. This occasionally happens to me and I can say that it has no clear relationship to the possible quality of the paper. In the case of the former (after review), the busy editor becomes a more likely candidate since the editor should study the reviews, decide on the faith of the paper, and possibly provide guidelines for your revisions.
If you have any indication, from for example peers, what typical handling periods are in the journal where you submitted your manuscript, you should definitely contact the journal to ask about the status of your submission. Such requests are commonplace (too common in fact) so try to assess if the two months is long or normal in the case of this particular journal before contact.