Transformers was originally owned by Marvel(yes, of Spider-Man and X-Men fame) as well as Takara and Hasbro. Marvel had the rights to all the names and likenesses, while Hasbro had the rights to all the toys (in North America) and Takara was the general rights holder. Transformers was actually originally release in North America as a crossover comic book with GI Joe

If you ever watch the Japanese release of the same episodes that we had from the first two seasons, you'll notice that there's a general drop in animation quality from the episodes that we had. Why this is, I'm not sure -- whether they were animated seperately (using keyframes) or they changed some stuff, but there is a difference, which leads me to believe that a lot of it was animated on both sides of the world, much like Armada. Another Tell-tale sign that is stereotypical of anime -- Transformers (the first seasons) was based in the United States. Unless the anime takes place on some other planet, or in another 'dimension', anime usually takes place in Japan. Everything after the third season takes place in Japan.

The whole thing began with an old toy line named Diaclones which I do believe had their own anime as well... they just recolored the toys and took out the human 'passengers' to make the Transformers.

So it is, and is not, Anime. However, everything after the third season (not including the last few episodes named "Rebirth") anime. This includes "Headmasters", "Masterforce", "Victory", the OAVs "Zone" and "Scramble City".. These weren't released over here.

Beast Wars (as we know it) was not popular in Japan. They had their own episodes that came out .. whether they were cel-shaded or not, I don't know, but they were in a more traditional 'cartoon' format. There were multiple instances of Beast Wars as well.. Beast Wars 2, Beast Wars Neo, and a few others. There was also a Beast Wars movie (again, in anime style)