Unique NobodyNaminé is not quite like the other human-shaped nobodies due to the strange conditions of her birth. Instead of simply being created when her counterpart became a heartless, Naminé was born from two people. Kairi did not become a heartless when she lost her heart because there was no darkness within her. Therefore, it went to Sora instead. It is assumed that Naminé was created from Sora's body after he frees Kairi's heart with Ansem's keyblade. Being created from Kairi's heart but Sora's body made Naminé different in two regards.
First, Ansem the Wise states in a secret report that she is a strange nobody because she did not have the memories or body a nobody is usually made from. In other words, Naminé was born without Kairi's memories. She had no awareness of who she was, what she was and what her purpose was. This lack of identity made it easy for Organization XIII to coerce her into doing what they wanted. What else could she do? Maybe it was not a path she enjoyed, but at least it was some sort of guidance in a world she knew nothing about. As she worked with the Organization and learned more about her powers that they wanted so badly, she began to realize who exactly she was.
As previously alluded to, the second difference is that Naminé was born with special powers. In place of having battle strength, she has control over Sora's memories. Not only can she change, add or delete his memories, but she can also effect those close to him as well. Naminé's abilities are eventually explained to Sora by Larxene and that she is often referred to as a "witch" because of them. Later on, Naminé also notes to Roxas that she has no idea why or how she was born with such powers and wonders if there is a right way to use them.
Naminé is also different from most other members of Organization XIII in one more fashion, though I do not believe it is related to the conditions of her birth. Similarly to Roxas and Axel, Naminé is shown on numerous occasions to have emotion. Loneliness is one of her prime motivators for following Organization XIII's orders despite not actually wanting to. She clearly feels guilty when she tells Sora the truth about his memories and Castle Oblivion and often looks forlorn throughout the timeline in Chain of Memories. Happiness and relief wash over her face when Sora forgives her for her actions and still wants to protect her regardless. Lastly, Naminé is shown crying when she says goodbye to Sora, knowing that he will no longer remember her and their time together once he woke up. Though we now know that nobodies have hearts due to Dream Drop Distance, Naminé seems to be more in touch with her emotions than most of the others. This connection may in part be due to her counterpart being Kairi. However, I also believe that part of the reason may result from how drastically different her situation is from the other nobodies. She was not indoctrinated by Xemnas' lies and other than her work for the Organization, she had nothing but her thoughts and feelings to occupy herself. Naminé is not driven by a "cause" like Organization XIII, but rather by emotions such as fear of being alone. Also, Naminé endures a more emotional situation than the members of the Organization as well. She is basically being held hostage and forced to do something cruel against her will rather than gaining membership to an organization with peers working toward a goal. Reasoning aside, Naminé most certainly experiences emotion.