Haibara/Shiho
Well.. after everything ShinRan have been through along anime/manga/movies... you expect them end up together.. but .. for me it'd be too boring.. and too obvious.. I expect some twists there. I imagine a relationship between Ran and Shinichi, and I imagine Ran being nothing else than a housewife, as her mother was when she still was with Kogoro. Eri is much better character being separated from her husband. Ran is too scary to be married or to be in a relationship with a detective who is always involved with corpses and murderers for her own sake she'd be better with someone else. I don't see Shinichi being the type of guy who goes to work after a giving a cheek kiss to his wife, and then going back home after work is done. I imagine Shinichi with Shiho traveling around, Shiho helping him solving cases, giving him hints like Haibara does to Conan, working for the FBI or the CIA ... the Ai/Con pair gives us a wider range of possibilities. For example, my favourite DC couple is Yusaku/Yukiko. I like how they do all sort of things together, like disguising themself to tease Conan, Yukiko being the night baroness, pretending be a detective, they share tastes I don't see that in ShinRan.
Plus Shiho, after losing every single member of her family, and since she was just a little child, having her life controlled by the BO and now being the main target of the same, no one else deserves to have a happier end than she does.
And to change a little, make the main character different from the rest, not childhood friend realationship.
Well.. this is just a humble opinion.