1. They are cousins, may be feeling familial bond than real love. Akemi did not seem to be aware of having any living family outside of her sister.
2. They did not start the relationship on the right foot with Shu using her for BO info. Lies are never a good way to begin any relationship over time Akemi may end up becoming bitter over this along with the secrets that Shu may have to keep while working as an FBI agent. Thereby dooming their relationship.
3. They live different lives. He lives in America and she is in Japan. I can't see him leaving the FBI, he is just too good at his job and he seems to genuinely enjoy the thrill that comes with it as well.
4. She does not know the real Shu as she was only familiar with a certain aspect of his personality (Dai) that he portrayed infront of her to gain her trust as a part of his mission. There is a lot more to his personality and character.
5. Had Akemi lived Shu would have had to likely arrest her for being apart of BO as she must have done some deeds for BO apart from being a hostage to control Shiho. Plus in the episode where she was killed Gin stated that they (BO) still had use for her sister. They had run out of use for her (Akemi).
6. Her mother made the initial poison which shrunk Mary Sera (Shu's mom) to a middle schooler. This puts them in an awkward position. Mary already distrusts Conan so may be cautious and not even fully embrace her in the family fold due to her history with the BO, the organization which may have killed her husband and still may want to hunt them down (AkaiVsGinVsRei) or use them to infiltrate their respective organizations (FBI&MI6).
7. Akemi comes across more as a dreamer than a realist. She believed that just by robbing a bank she could free her little sister from BO's control when she knew full well that her her parents had been kept under close scrutiny since they began working the the APTX 4869 drug. She was also separated from her sister after their deaths and used as a hostage to motivate Shiho. She chose to act alone and not to seek help from Shu. He would have probably come up with something more realistic and reasonable like faking her death to weaken BO's hold over Shiho and later on save her as well from taking the poison out of despair.
1. In Japan first cousins being in a relationship is considered to be okay and the same goes for Britain.
2. She knows and has accepted that he used her but still wanted a chance to start over.
3. She can move to America or Shu can leave FBI after the end of BO.
4. She could try to get to know Shu as she had asked in her message if he would consider being her real boyfriend.
5. She can make a plea deal and do some time (a few months/minimum years) behind bars as she was also a victim of BO.
6. Both the aunt and niece can together grieve over the loss of their shared loved one (sister & mother).
7. Being a dreamer is not a bad thing she could give Shu a hope to fight for a better future and look at life from a different perspective, less cynical (if she had survived).
1. They do not have to worry about being of the same blood. One cannot choose family but they can certainly choose their friends and partners, Shukichi Haneda firmly believes hat he has found his happy ending with Yumi.
2. They were both likely aware of what they were getting into when they started the relationship. i.e their pasts as well as loss of their parents and the urge to bring justice. These topics may have come up over time.
3. They are both American citizens and work in the same environment so less probability of uprooting. She understands the risks and that come with the job. She did not freak out on Shu when he gave her his infamous line of not being able to love two women at the same time. Plus, him faking his death to protect his team. Any other woman may have likely screamed or punched him for pulling such a stunt. Although I believe that she was in shock after the whole chase that she and Camel had to endure because of Rei. She was also initially portrayed as a mysterious and smart character who encouraged Ran to solve a case when she was unable to get a hold of Shinichi. Plus explain the hidden photos of the students as well. She has a lot of potential but the writer needs to use her more than just make her cry over Akai.
4. She was targeted by both Vermouth and Bourbon to get to confirm Shu's death.
5. She knows more about him than most, the good, the bad and even ugly ("To be able to love two women at the same time…it's not that handy a personality.) She has been supportive through it all.
6. No criminal background.
7. She poses less of danger to Shu and is also a trusted colleague. So, less likely to come under Mary's line of fire and may even sympathize with her loss (Jodie's parents death) being similar to that of the loss of her husband.
8. Bonus - Gosho would not have slipped the info of ShuJo being previously in a relationship if he was not planning to sew in more details later. For example, Camel has been highly emotional regarding Akai, with time it was revealed he had accidentally blown his cover as Dai. Similarly the case was also with Masumi whose entry lead to the intro of Shu's mom and her being a victim of APTX 4869 like Conan and Haibara. Plus, do check out Detective Conan Ending 64 - Veronica (By Mari Kuraki) where ShuxJodie are shown together. So, there is possibly more to come. After all one truth prevails<3