My impression is that the quality of training from individual dojos and teachers is often more important than the differences between organizations.
I would do more research about the specific dojos and teachers you're considering from both organizations, visit and watch a few classes, perhaps try a class, and make decisions based on what you find.
I completely agree with this. I have changed style 3 times now, and each time it has been for the individual teachers, not because I liked one style over another. In general, I think Peter is correct. You will get a lot more structure and precision in Yoshinkan. The downside is that, depending on the teacher, this can lead to being overly rigid and tense. Not all Yoshinkan teachers are like that though, and if you find a good one it would be worth trying.