If you are a PC user than you can just make a macro for embrace and put it where you want it as this will work for both fairies. Is you are a PS3 user I am not sure if they fixed it in that hot fix when they reverted the allagan gear but they can't macro selene's embrace and just have to deal with it for now.

Also, I was like you and loved being to manually command EVERYTHING. However, the current system has the fairies no matter what combination of stances you put them in autoing Embrace so you will never be able to 100% manual anymore.