Beast Wars is my favourite of the lot, if a bit goofy at times. Generation 1 is very badly dated (it has the usual poor animation and one-off episode plots of most '80s shows) but it's great for what it is, especially compared to some of the series that followed it.
The Japanese ones (Robots in Disguise, Armada, Energon, Cybertron) are often cited as the worst in the series, but I was more offended by the preachy, pretentious betrayal that is Beast Machines. The Japanese shows were written for foreign tastes and then hurriedly adapted into English; Beast Machines has no such excuse.
My biggest problem with all the shows after Beast Wars is the obsession with including child/teen characters. The logic behind this is to make the shows more appealing to children, I guess, but even when I was a child myself I resented these characters and would have been happier without them. Transformers: Prime seems to be the worst of all in this regard, frequently relying on the children doing stupid things as the basis for an episode's plot, and Season 2's finale ultimately hinges on them rather than the giant robots the show is supposedly all about (seemingly crushing hopes and dreams of a Season 3 set on Cybertron--but of course that would mean saying goodbye to the children, and we can't have that).
Post edited November 20, 2012 by Arkose