Bit of a random thought, as publishing in either is good of course. I do not intend to demean anyone who has published in special issues.
I can think of pros and cons from one to the other:
Special issues may get more exposure from people searching within a collection. However, these tend to be offered through invitation, which often or not, the submitted paper may less likely be rejected. This means the quality has a potential to be of lower standard.
Regular issues in this instance may be harder to get accepted, especially in high impact journals, as many researchers will try to submit their work to the journal. Would this mean some people view special issues from invitations as a "free paper"? Where publications in regular issues may be more "genuine"?