I think when discussing atemi we have to look at O Sensei's aikido. If you have seen his demonstrations on tape you notice that you can barely tell who moves first his uke or himself. I think sometimes we forget the martial aspect of "Illiciting a prescribed response". I teach kicks (from the midsection down), strikes to maintain distance as well as getting uke to break their own balance.
I truly believe that as you progress in aikido you will develop your own "type" of atemi. Whether this involves punches, kicks, entering quickly with breathpower, a kiai, or a myriad of other things. Each practicioner will find a way to make his or her aikido effective in a martial aspect, if this is part of their goal when training in aikido.
Just my humble opinion,