My feeling is that the general goals of Roppokai aikijujutsu and Aikido are different.
I have to agree with what Jorge has said in regards to the goals being different. When discussing method / technique / waza / structure, the discussion inevitably, and rightfully, boils down to how one method compares to another in achieving a particular goal. Not, what is better or worse, just how things are approached and what are the benefits / drawback of each method. If the goals are different, however, this dialogue becomes moot. If we are looking to achieve different goals, it stands to reason our approaches are also different.
Although DRAJJ obviously fills volumes when writing the history of Aikido; Today they are very different arts whose goals may not be the same.