The most notable difference that I remember between Rowan and Citra is that Rowan seemed more absolutely determined, while Citra seemed to carry some determination, albeit with compassion more prominent. This brings into question the idea of worthiness for being a Scythe - since a Scythe is able to kill people at a whim with no repercussions, perhaps even with praise, should one value compassion or absolute unbiased determination? Objectively, Rowan is better fit - he is more determined and able to take lives due to his nature. This will be seen later on in the book if you read what happens to him in the future. However, as compassion is needed when interacting with others, especially given a difficult idea such as killing, Citra may be a better fit, as she can be empathetic to those who are in the position of being gleaned.
TL;DR: It depends on your point of view. Both are good candidates, as Faraday asserts simply by choosing them to be his apprentices.
