Now Doom? Doom wasn't a bad villain. Far from the best one either, but he served his purpose well. His role in Shadow's story was decent and not overbearing. His personality fit him well.
Doom was better here than Eggman was. In this one case, Eggman seemed like an accessory to the story. His particular arc wasn't bad, but didn't seem to add too much to the overall atmosphere, at least to me.
It "made sense," but Eggman was the least important threat in the entire game.