Fantastic Four, Spider-Man, Batman Begins and so on are not truly movies based on an animated series. They're movies based on the comic books that the animated series were based on.
For example, there were some nods to B:TAS in Batman Begins (the ski mask from "Mask of the Phantasm", the train fight from "Never Fear"), but overall the movie was grounded in comic works like "Batman: Year One" and "The Man Who Falls."
Transformers wasn't based on a single animated series either, but on 20+ years of shows, comics, novels and toy packages. More of the Transformers mythos in the movie came from the comics than the show. The main plot was basically borrowed from the 2005 comic arc, "Infiltration." Other concepts (like Sparks in their chests and the word "Allspark") came from Beast Wars and Beast Machines.
And for the record, while Fantastic Four was a dissapointing movie, it was better than ANY of the animated incarnations of their origin. Watch the pilot of the 1990s series to see what I mean. Horrible. The 70s series had its moments, but it was hindered by the gosh-awful production qualities of its era. Season 2 of the 90s series was the closest thing we've ever gotten to a good, comic-based series. The modern show just looks terrible, though I haven't seen enough to judge its story content.