GI Joe has gone through many, many changes from Eco Terrorism to the Ninja thing. Read some of the comics.
The difference is, all those sub-lines of Joe toys came out in the same set "universe" as the original "Real American Hero" line. "Transformers" has made several clear continuity breaks in its time. Within G1 there were already at least four distinct timelines. G1 is a totally separate entity from the "Unicron" trilogy (though the "Unicron" trilogy does reference some G1 stuff, mostly as a nod to fans more than continuity). Those series are themselves separate from "Robots in Disguise" and so on.