As you mention in your description of your dilemma, while the two profiles have similarities suggesting they may be for the same person, there are also some discrepancies suggesting they may be two different people with similar names. Since, it's fairly common to find people with similar names and backgrounds in nearby localities, it seems that further investigation is needed before you should merge.
As Ellen Curnes suggested, you should try contacting the profile manager, if one exists. You can also look more at relatives of each of the individuals in the two profiles. You've noted the similarities and differences in names of each man's son and wife, but what about birth dates and places? Are there other distinguishing features or relatives? Who are the relatives attached to each of the related profiles? For example, do John and Jonathan have children, and do those children match?
Personally, I don't think it's wise to merge two profiles unless you are certain that they are the same person. That can create a lot of confusion, which will take a lot of work to correct. Of course, if you are certain, then merging means more connections, which is a wonderful thing.