The first Transformers series had a Japanese dub that dropped the fourth season, and replaced itself with new episodes and various continuation series.
Beast Wars had gender changes, and a rewritten script to make the series more comedic, and less dark. The series had extended continuity with Beast Wars II, Beast Wars II: The Movie, and Beast Wars Neo. Both of which were more comedic than the original show. The gender change of Airrazor from a woman into a man creates some awkward moments in later portions of the show, where her, and her lover, Tigatron fuse. The Japanese dub says they're brothers.
Animated is having heavy story/character re-writes to link the show to the Michael Bay movies. Characters have been renamed to characters that are also in the show (Bulkhead was renamed Ironhide, despite the fact there already is an Ironhide in the show...), and they will be airing episodes out of order, which will be creating continuity errors. We don't know if they're doing anything to the mood of the show, as we've yet to see an episode air.