(Full disclosure: I liked Yoshino better)
Thinking about the story as a whole, man this was poorly written and paced. Which also makes no sense since he was only responsible for the writing while Tiv did the art, so he should have had plenty of time for story structure. While I think some of the seeds of Yoshino being a romantic choice were there early on, it was very very minor, which made that eventual build towards Yoshino not mesh well with what came before. Even if I think, in hindsight, they built a really good rapport with each other. Yoshino being assertive with Makabe was an act and with that pretense dropped it would have been a very nice relationship.
The problem with how the Aki ending is wrapped up is he left a lot of loose character development threads dangling. This series could really do for a light novel re-write where he properly structures shit and ties up the development. The real payoff we needed for the Aki ending was to have them move beyond their past. While I would say Yoshino viewed Makabe in the "now"... After having the truth revealed, Aki was still seeing the Makabe of the past. Yes, they mention that as a problem with the whole "this is who I am now" scene, but we never actually see it addressed by her in any concrete way. Then we have the whole mess with the Yoshino-arc muddling the waters with him dreaming about her, pseudo-confessing to her, having the hives reaction to Aki that was never addressed, etc. We really needed a lot more time of Aki learning to be more independent and mending her relationship with Yoshino on a more equal footing. (I was honestly expecting her to fire/release Yoshino. Expecting a young child to serve another girl their entire life in this day and age is cruel imho. It's not a family business like a bakery.)
There are the seeds of a good story in this mess, but it was very poorly executed IMHO.