I'm not trying to provoke an argument or set people up to flame their tastes, but honestly, what were the episodes that were not just good strories, but were cerebral and thought provoking? What's the list?
I think there's probably more to say on the topic than simply reducing it to "good stories" versus "some type of cerebral, thought-provoking thing that obviously never existed."
Star Trek can tell a variety of different types of stories in what basically amounts to a fun, pulp sci-fi format. I think it's a little unusual among the big pop culture franchises in that it doesn't rely as heavily on a "hero/villain, good guy/bad guy" approach.
It does have that, of course, but a lot of Trek stories draw pretty heavily on other types of structures, such as: exploring the unknown, heroes vs. environment, heroes versus their own demons, heroes' ideals versus some internal or external threat, etc.
I think, a lot of the time, when fans talk about Trek's "cerebral" or "thought-provoking" side, part of what they mean is something like: I enjoy these other types of stories, partly because I can engage with them intellectually a bit more, while still having a good time.
It's not so simple as: "entertainment" versus "something more serious, which Star Trek has never been." Entertainment varies a lot in terms of quality, and not just on a technical level. Often it *is* more fun when entertainment can be engaged with intellectually, at least to a degree.
I'd rather watch The Avengers than Transformers 3, and one reason is: The Avengers is a huge blockbuster that is written and filmed in such a way that I don't have to turn my brain off to enjoy it. It's not insulting my intelligence and assaulting my brain at every turn. There is a difference, but it's not "entertainment" versus "serious philosophical business."
I've enjoyed Trek over the years because it has generally been entertainment I can enjoy for a few different reasons, and one of them is: often, I can leave my brain on. It's possible for entertainment to be entertaining and also play around with some interesting ideas. A lot of the best entertainment actually does, in one way or another.
Anyway, looking forward to this movie whatever it may be