My guess is a few things.
1. There was no cartoon at that time.
2. Some of the older Joe collectors were starting to bitch now that they were adults and collecting as a hobby, demanding that they wanted more military and less sci-fi.
3.Too much Ninja stuff that was poorly executed. Some of the designs for the next Ninja wave that was gonna drop just looked bland. They were even gonna do a Ninja Baroness, but it just looked weird having her in the outfit they gave her, even though the head sculpt was great for it's time.
So, they cancelled the line and tried to give Joe fans what they demanded, A WWII style like called Sgt. Savage that ended up not selling well.
I think the Sgt. Savage line tanked mainly because it was out of scale with the previous figures and had no cartoon though.