I am familiar with both. ISSA will delve into the strength curve and understanding the science behind force production. NESTA will not cover this in any kind of depth, but NESTA has a progressive model for training, steps if you will, for progressing a client. ISSA teaches you principles to develop your own training model. ISSA will give you all of weiders principles of training, NESTA will make no mention of these nor will most certifications.
If you want a system laid out for you go with NESTA, if you have a good understanding of programming and want to know more about the science of the strength curve then go with ISSA.
I am ISSA certified and it is a solid certification, I wish they had a progression model though for beginning trainers. I was at one time MMA Conditioning Association (an off shoot of NESTA) and they use the same training model, the NESTA Cert is a solid certification and you can’t go wrong with it.
The ISSA exam is more practical and will require you to do some research, NESTA is multiple choice as are most NCCA certifications.