The most important influence on royal marriages in the 16th century (and many other centuries) was political needs.  Royal families married their children off in order to improve their political situations.

As an example of this, we can look at the events that led to the St. Bartholomew's Day Massacre in France in 1562.  The massacre happened at a time when it had been thought that the Catholics and the Calvinists of France had been reconciled to one another because of the marriage of Charles IX (Catholic king of France) to Henry of Navarre (a Calvinist).  This was a marriage that was made in part to heal religious differences.

We can also see this in the marriage of Henry VIII and Catherine of Aragon.  Catherine's parents had unified Spain and then started to marry their children in ways that were meant to make alliances with other countries.   They had various children marry royalty from places like Austria and Portugal.  In addition, Catherine was betrothed to Henry's older brother, Arthur, who was set to become King of England.  After Arthur's death, Catherine came to be married to Henry to improve relations between Spain and England.