So you haven't seen TNG, Voyager or Enterprise? The central point of your comment dissolves with the fact that many episodes gripe with the prime directive. Many of the best TNG episodes grapple with morality and tackle complex issues centering around incorrectly applying our values to other cultures. Alongside that, culture and authoritarianism, reflections and warnings of what can happen to even societies that see themselves as enlightened (Drumhead comes to mind).

I think it's important to critique shows within the context of the eras and societies they come from but you don't strike me as someone who knows the star trek universe very well.