Ewen, do you practice Dentokan Jujutsu? Your name seems familiar. Aikido and Hakko-Ryu training methods are fundamentally different. Hakko-Ryu, especially mainline, almost exclusively focuses on paired kata training and is far less "organic" than many of the popular styles of Aikido.
With that being said you're also going to see a large variation in training methods between dojo's that practice offshoots of Hakko-Ryu (like Dentokan and KoKoDo). Our training regularly includes "spirited" jiyuwaza and randori training, while many other Dentokan groups tend to focus more on kihon-waza.
We have some Aikidoka that train with us and there is definitely a benefit in participating in both arts. Jujutsu practitioners can certainly benefit from the movement found in Aikido.
You might try searching for some Roy Dean articles as he has written a bit about training in both Aikido and Seibukan Jujutsu (another off-shoot of Hakko-Ryu).
Yes I do train in Dentokan Aiki-Jujutsu and from your description it is very accurate, we almost exclusively train paired kata style. While training methods are fundamentally different they are still based on a symbiotic relationship between uke and tori. I enjoy training in the waza techniques of Aiki-Jujutsu, however I feel that the art could benefit from incorporating randori into the training methodology but perhaps it would be too difficult an adjustment to make without making the kata work more organic as you said?
Correct me if I'm wrong but from my observations Aiki-Jujutsu seems to concentrate on what to do once the uke has a firm hold of tori, whereas in Aikido it is more about intercepting uke's attack creating the motion?
Incidently, I am a huge fan of Roy Dean, I think he is an inspirational martial artist and I own a couple of his dvds - art of the wristlock and white belt bible. He is one of the reasons I am pursuing cross-training in Aikido.