You have asked an excellent question - and I'm not sure there's one good answer to give you, because we are still discovering benefits for both. I can tell you that CDS does not work on malaria like MMS does - CDS seems to have some particular applications on skin issues.
I can tell you that CDS is easier to take, in terms of taste and smell, than MMS. I can tell you that if I were doing injections, I'd only use CDS. Another question, also, would be what differences do the stabilized CDS create, and what about different ways of making MMS - such as Scott's 7 day fridge method - The question then becomes WHY do we have these differences? We are still continuing to find out. We have had testimonials for health recovery with both products.
Personally - If it were me and I were dealing with a major disorder, I would start with MMS, low dose and build slowly - if I had problems with the MMS that a change in activator didn't handle, I'd go to the CDS. But this is just my opinion. For maintenance doses or smaller issues, I tend to use the CDS - After years of trial, I prefer to use MMS to brush my teeth, as an example -
MMS can be made with several different activators, and quite a few techniques. CDS also has variations available to it. MMS you have to keep away from light - CDS needs to be kept cool (and away from light) - It is easier for CDS to lose it's potency than MMS.
I know I'm not answering your question in the way you wanted, but there's a much bigger picture here. One thing - you can easily make CDS from MMS and citric acid, or MMS and HCl.