Common themes:
1. Toys are not as popular as they once were, due to various factors (Video games, attention spans, lack of imagination, etc).
2. Believe it or not, the collector community can't sustain a line by itself (At least not one pretending to be a mass market line).
3. RoC toys must have massively undersold what they projected (I think we could see that coming with all the stock left hanging around and at clearance stores!).
With that being said, I assume they are trying to go "Ninjatastic" with the Retaliation figures in hopes of catching kids attention. Adding crap in just to make a quick sale, not to really get the kids as fans of the property. No file cards, no personality in the packaging, nothing that's made GI JOE.. well, GI JOE. They're flashy "action" figures, with The Rock's mug on all the packaging, and lots of explosions. Mutable explosions, per package!
Rise of Cobra at least was true to the collector base with their figures, and who knows, maybe that's why they bombed at retail? (Or it could be the fact that stores got about 2 billion wave 1/2 cases and 3 cases of everything after?). They seem to be taking a different approach, so we'll see how it goes.. I bet a lot of people thought that the Bayformers Transformers line was gonna bomb, and look how it invigorated the whole property.. I think they're hoping for something like that (Though how they plan to get there by taking away features.. who knows..).