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.
How far have you gotten into the curriculum? I feel like once you get into Sandan and Yondan things start to make more sense and you can start to see how the kihon-waza can be applied in varying situations (especially with attacks that require you to enter/receive/blend). We do practice a great deal of oyo-waza which really helps things make sense in my opinion.
However, I totally see your point in regards to the attacks in the paired kata. It involves a great deal of static positioning. You have to keep in mind though the intention of the training method is to be able to learn to perform the technique as flawlessly as possible in a short amount of time. With that in mind it is much easier to learn Ude Osae Dori if the attack is a grab as opposed to gedan tsuki. If a strike is coming you have to factor in how to receive that strike. That adds more to the equation. The KISS theory applies.
It was explained to me that this is why in each set you go from seated to half-standing to standing. When you first learn to perform the technique there are less variables involved in the interaction between tori and uke. By the time you progress to the standing versions of the techniques you should feel fundamentally comfortable and have a good feeling of how your posture should be and how to use your hips to move uke. Imagine if you first learned how to do Ude Osae Dori standing as opposed to seated. If you couldn't manage to take uke's center you could simply cheat and step out to force them to break their posture. However, in seiza you are forced to learn the proper method or the technique.
Could you perform Ude Osae Dori from a strike? If you have a strong grasp of the kihon-waza, of course. However, you have to be in an environment where you have the opportunity to experiment with responding to various attacks (jiyu-waza/randori). If your group focuses exclusively on the kata you may want to bring up the issue. Myself and another yudansha in our group decided we wanted to include more jiyu-waza in our training so we took it upon ourselves to work on it together.