Quality entertainment vs. polemical shovels to the face
Interesting that you'd bring up "Atlas Shrugged"... I enjoyed it a good deal more than you evidently did, but I wasn't blind to its flaws. (Absurdly stiff and didactic heroes, to be sure, but the villains did have a certain chilling plausibility.) For the purposes of this discussion, it's important to note that those flaws were unnecessary, and they got in the way of whatever else the movie was trying to accomplish.
It's not so much a question of production values - it was a low-budget movie, but it looked good enough. Better actors would have helped. Was that more a question of budget limitations, or did it signal the need for more creative casting agents? (I haven't seen Part 2 yet, but I understand they used a different cast, so maybe that issue has been addressed.)
Above all else, "Atlas Shrugged" suffered from being a clumsy adaptation. The problem was screenwriting, and that doesn't have to be an expensive problem to fix. (I don't hear a lot of talk about super-rich screenwriters.) More specifically, the writers did not do a good job of intriguing the audience and drawing them into the story. It was, as you noted, a polemical shovel in the face from the very first scene.
Just to highlight the most glaring flaw, John Galt should have been a compelling figure of mystery. The disappearances he was involved in should have been left a sinister enigma until a huge, stunning reveal at the end of the film. The audience should have been intensely curious to know what he was up to, and fearful that it was something utterly nefarious. Was he killing those people? Why did he target those people? The "hook" for this story should not have been so frail that it left anyone checking their watch or wandering out of the theater, especially not when that hook is summed up in a tag line that appealed to generations of fans, and was prominently featured in advertising for the movie: "Who is John Galt?"
We could pick apart all sorts of other problems with "Atlas Shrugged," but the bottom line is that excessive fidelity to the source material kept them from crafting an interesting adaptation within the time constraints of a movie, crafted in a way that would invite those unfamiliar with the story to follow its narrative. (With all due respect to the Ayn Rand fan base, I think the whole story could have been tackled in one film, with sufficient trimming.)
As I wrote earlier, you can give an audience questions as a gift, but they recoil when answers are shoved down their throats, as countless liberal polemicist filmmakers have learned to their sorrow. Less didactic protagonists who undertake a compelling personal journey to solve a great mystery could have been used to invite "Atlas Shrugged" viewers along for a memorable experience. Ideology-spouting robots are not going to win over many people who didn't already know the story, and just wanted to see it recited by well-tailored actors.