Seems to me that during "warm ups" several different processes are occurring. Some are short-term preparation (e.g., increasing muscle temp.) while others are longer-term training (e.g. increasing ROM or strength). Possible aims for aikido warm up exercises might be:
Motor skills training.
Mental preparation (calm down, hype up, get in the right frame of mind)
Muscle strength training.
So I guess the question is what do you want; and I think we can agree to differ here; and what is the best way of achieving it (the science bit)?
On a personal note I have found that my understanding of many of the aiki warm up exercises has changed over the years. I now view many of them as educational tools, and see them in a more meditative light. One instructor I know asks students to "listen" to their bodies during warm ups so they can learn from them. Warm ups can be aikido not just preparation for it.
Re. breathing exercises, aikido seems to me like one big breathing exercise/ massage, whatever the style.