Taking a pseudonym for publication
It can be a very real problem later on, when you will be looking for a job and potential academic employer, or just colleagues, will want to check on your academic record. Changing your name to make it unique might also bring you a lot of trouble later, as your employing institution will not easily access your publications (knowing you by a different name than the one appearing on you publications).

However, it could very well be that, given the practice of your field of research, you could avoid changing the spelling your name. Usually, journals will take your second (and possibly third) name into consideration, and use it for all indexing purpose. At that point, your abbreviated name could simply be unique, no matter how common your first and last names!

For instance, John Andrew James Smith would be abbreviated and indexed as JAJ Smith, for which even PubMed does not even returns a hit! (PubMed covers most of life and material sciences)