It seems to me that there is just SO much to learn in aikido before I can even think of atemi.
As well as being used for distraction, over focus on atemi can itself be a distraction from the lessons to be learned from Aikido.
Some balance is needed.
Atemi is easy to see and understand. Aligned with irimi then it creates great potential.
Other things are not so obvious and need to be worked at during practice. Adding to Stefans post above someone who constantly uses full or near full atemi will soon run out of willing partners and also can easily miss the subtleties available through practicing with less focus on atemi.
IMO - For fighting atemi is a must have, but is the practice of Aikido for fighting?
I'll toss that up for others to chew over...or not.