It just seems much more logical for Ferdinand to 'get' the Netherlands because it's so much closer to the realms he got. Why did Charles V give it to Phillip II, seeing as it was relatively far away from Spain and Naples? Was it some smart political decision or for another reason?
A reply to /u/notavriend (Schild en vriend)
This was asked quite recently here, so a revisit may be good.
Charles V had significant reservations over how the Low Countries should be inherited. Between the strong local governments and the difficulty of access from Spain, having determined above all else that his son Philip II should be King of Spain's crowns, the question is how he should handle the Low Countries.
There were many arguments between him and his brother Ferdinand and his son Philip II. The larger disagreements include how the HRE emperorship should be handled. Ferdinand wanted to keep it in his line of the family. Charles wanted a sort of time share. Philip wisely went around his own father to negotiate in Ferdinand's favor in order to preserve harmony in the family..
Charles V knew that the hold on the Low Countries would be untenable if England was not on Philip's side. So he asked Philip to join him there and then to decide for himself wherever he wanted that inheritance.
Philip duly came and decided he did want the inheritance. Charles V then arranged for Philip, a recent widow, to be married to Mary Tudor, Catholic queen of England. They then became co rulers of both England and the Low Countries. This was the so-called "Northern Orbit" strategy. The hope was that it would set a lasting (Catholic) alliance between Spain, England, and the Low Countries. Of course, Mary died without an heir, and the Dutch revolt broke out, turning this arrangement into disarray.
But there were several ideas that were floated over time. Charles suggested that his daughter Mary should inherit the Low Countries, and Ferdinand's daughter Milan, and that one of them should be married to a French prince Duc d'Orleans. Unfortunately, the Duke died not long after this idea and political settlement was floated.
Regardless, as soon as Philip decided he wanted to inherit the Low Countries, Charles V had to make several other pieces move, including the Pragmatic Sanction, the inheritance of Milan (in order to secure access from the Mediterranean to the Low Countries), and so on and so forth. This was at a time he was physically and mentally exhausted.
If you're interested in Charles V and Philip II you should check out some of the questions I've answered on my profile page.