honestly the real difference between certifications is MONEY. That's all these organizations care about. In the real world, a certification is a certification....your clients don't know the difference between ISSA, ACSM, ACE, or C.R.A.P.... as long as you can produce results and have credibility. Besides, most people see that if you have the initials CPT after your name, then that's good enough for them. You're special. So in this case, go for the cheapest to save yourself money..... take an online course for $50 if possible.
I say "real world" because we're talking about people who just want to get in shape, and/or lose weight, etc. The majority of your clientelle. There are gyms who will only hire trainers with certain certifications, but there are others who'll take almost anybody. I would personally try to work for myself since all the profit would go to me.