Having spent significant time on the Mass Effect forums, it seems that most players on the BSN proclaiming Shepard is an idiot are upset for really two reasons.
Mostly, because people are convinced it would be good writing for Shepard to come up with a magical solution to the Reapers (build a super-duper fleet, super-duper weapon, use a super-duper tactic.) Basically, forum members upset with the Crucible and Catalyst (which is fine, so am I) convinced that the have the answers to everyone's problems and demand Shepard is 'stupid' for not implementing them. . Needless to say, these 'solutions' (often shilled as brilliant science by forum posters) are not only generally ridiculous on a technical level, but worse, completely garbage writing.
You know, on second thought, it's really less people being 'convinced' and more just desperation. People flinging out ideas in desperation of having something, anything, other than the endings. These ideas just aren't good enough to stand on their own, so they have to be shilled.
Aside from that, it really seems to be frustration over people not liking the autodialogue response. Which is fine. However, it's less fine to pretend that Shepard not acting like your ideal imaged character is 'stupid' instead of just out of character.