It also doesn't help that Transformers have (from what I can tell) a fragmented fanbase.
We've already talked about the movie/animated split, but then there's fans of the vehicle figures that probably couldn't care less about Beast Wars, or fans of one of Cartoon Network's latest Transformers cartoons and wanted to see more cartoon-styled (well, cartoon compatable) Bumblebees.
Then there's the inherent weirdness of a line of Transformers that doesn't actually transform. It's been done before, but it doesn't make it less weird.
Having seen a number of these lines come out now, it looks like having a wide character base is one of the most important factors. Lines like SHS and Galactic Heroes can do well, because you can invest in some unique sculpts, put out some repaints to keep the "named" characters (the Spider-Men and Lukes) available for casual consumers and use those to subsidize character depth.
Marvel has a ton of names they can use to subsidize new characters (Spider-Man, Wolverine, Iron Man, Hulk, and to a lesser extent Human Torch, Thing, Captain America, Thor) and so does Star Wars (Luke, Han, Leia, Darth, Chewie, Anakin, Obi-Wan) but for lines like Combat Heroes and Robot Heroes, if you get too far from Snake Eyes, Stormshadow, Cobra Commander, Optimus Prime, Bumblebee, Starscream and Megatron... you end up going picking a market at the exclusion of others. Nostalgia buyers versus casual toy buyers versus movie fans versus long-time collectors of the individual properties or of a certain generation.
But I still think the Universe line deserves a second chance. Balance movie, G1, Beast Wars, Beast Machines, versions based on cool unreleased Japanese stuff. That way everyone gets something.