Can I ask the journal to publish my paper in a later issue? Say I have submitted a paper, it got accepted, but for whatever reason I would like to publish this not in the next issue, but in a future issue. 

Could I ask the publisher to do this, or would this be considered rude? How would I best ask for something like this?
Speaking as somebody involved in journal editing, I would find such a request unusual but not rude per se. The most important part of making the request would be providing a clear and well-justified explanation for why you want to make sure a variation.  There are, in fact, legitimate reasons that somebody might request a delay, such as:


Since the initial submission, a decision has been made to file a patent, and the delay is necessary to have time to complete the filing (so as to prevent the patent from being invalidated by public disclosure).
The article is intended to be co-published with another article derived from the same work.  For example, this is often done by large physics collaborations.  Usually, the journal should already be aware of this and planning for it based on the initial submission's cover letter, but mistakes can happen.
The authors have discovered a possible error and want to delay publication to resolve the question rather than risk a correction or retraction.


I think it is likely that most strong and reputable journals would be willing to make reasonable accommodations for situations such as these. For bad reasons (e.g., you want to see if your paper will be accepted by another journal that you dual-submitted to), expect to have your request ignored or to face more severe consequences.

Even if you have what you feel is a quite appropriate and reasonable request, however, be prepared for the possibility that the journal may be unwilling to accommodate your request for its own reasons. Publication, remember, is largely a voluntary association on both sides. In this case, you may be faced with a decision to publish on the journal's schedule or to withdraw the submission---or the journal may even make that choice for you, and not in the way that you prefer.