Franchises
A franchise, for lack of a better term, is an incarnation or "generation" of the Transformers brand. The word is used here to refer to the collection of not just toys, but also media, merchandise, and ideas that surround each of these incarnations. Because of these other elements, the word "toyline" would not be broad enough -- the toyline is just the toy component of the whole thing.
Franchises within franchises
Beginning with the third year of Generation 1, Takara got into the habit of annually rebranding the Transformers property. Moreover, 1987's The Headmasters kicked off a trend in which Takara's toylines and fiction branched off from Hasbro's versions to increasingly significant degrees. Thus, the later iterations of Japanese G1 are often referred to as "franchises", despite being part of the larger G1 generation.
A similar situation arose during Beast Wars, when Takara decided to augment that series with the Japanese-exclusive franchises Beast Wars II and Beast Wars Neo.


