Most of the really good Trek shows are stories that are ambitious enough to draw some inspiration from - the heavy "message" shows were
always awful.
"The Doomsday Machine," for example, was a story about an obsessed character. That it bore the standard observation that people shouldn't play with big things that go "Boom!" is trivial.
As for the new movie being a potential embarrassment...if I were really capable of being embarrassed by "Star Trek" I'd have never looked back after "Patterns Of Force."
..then you're just like that BBC culture reviewer who was annoyed by the message in Wallee.
Star Trek is primarily a message filled, morality show. Every single episode has a message. Perhaps some could watch Encounter and see that it was just about the new enterprise being able to split in two and seeing the Enterprise's new photon torpedoes. Others may see that it is about the farpoint creatures that can disguise themselves as space stations. Some may even take some notice of the considerable chunk of Q and Picard's dialogue that talks of humanity's progression from a savage race.
Gene Roddenberry said at the beginning that Star Trek was a 'Wagon Train to the Stars' - it was a vehicle for discussing morality issues. Every ST up to this point has been like this and if it is lost, it will not be ST.
I think it will be toned back a bit in ST11 and some people won't even be able to see it. We live in selfish, amoral times.