Trek really jumped the shark when it began overstaying it's welcome. I think that occurred with Voyager and Enterprise more than anything. Sure, they had some decent episodes, but they just weren't fresh or interesting enough.
In Hollywood they say that "the last sequel, is the one to lose money." They said it after "Jaws 4," but a there's more than one way to jump a shark.
When Roddebberry left, then the series became an empty franchise; but when he came back it was preachy rather than intriguiing, and I get the feelng he just became a figurehead like Roy Disney, and didn't have any of his original creative staff like Nimoy or the rest.