Please don´t be offended. Seriously. I find it a bit comical that someone might suggest atemi as an effective method of dealing with BJJ or shootfighting (as someone has already mentioned). For the record, I´m in Brazil, train BJJ too, and can tell you that the first two things we learn how to do here is avoid getting kneed or punched severely in the face when entering an attack, and the armlock. Along that line... if the attack doesn´t connect causing at least minor head trauma... your going down! When a shoot occurs, the head isn´t usually in front of the knee but rather to one side guarded by the shoulder. Most Aikidoka just aren´t prone to turn kickboxer mid-attack and would probably go down while trying to punch or kick the incoming head. One consolation is that Aikido is extremely similar to JJ (speaking in terms of locks and joint manipulations, nothing else). Much of the Aikidoka´s arsenal exists in JJ. Ude-hishigi=Armlock kote-gaeshi=mao de vaca. etc. Aikido can work on the ground. The difference is that Aikido doesn´t train ground and doesn´t train leg locks. OOps... I rambled...sorry...
The point: It could be worthwhile to do something about a possible lack of ground-fighting ability.
At your service,
Post Scriptum- There is weakness in everyone´s Aikido.