I think it's kind of interesting that I chose Rowan's first name to be her short name, whereas with Locke it is his surname that is the short one. It changes the in-game interactions with NPCs and such. For example, Admiral Quinn generally addresses people by their short names. His use of "Rowan" seems to indicate an avuncular relationship, as if he is a mentor or family friend. He addresses Locke by his last name (a common practice in the U.S. Army, if not all the armed services) which shows a possibly friendly but certainly more distant relationship.
Rowan's "personality" (as I imagine her) allows for this kind of address. She is more casual about Starfleet protocol than Locke, who is very much the military man. I do like that STO includes long names, as there are occasions when NPCs do use them as appropriate. I seem to recall at least one of the quest givers addressing Rowan as Lieutenant Starblanket. Plus, the promotion ceremony dude at Earth Starbase uses the full name, as is appropriate for a formal occasion.
Which name do you use for your captain's short name. Does he or she have a full name as well?