Crew will be changed out over time, like real-life ships. This could be due to a crew member dying on a mission, or transferred out due to needs of the service. The actors would have multi-year contracts, and when their character is changed out they become one of the masked aliens seen in the episodes. This prevents people from guessing that the actor with the 1-year contract will be one to die/leave.
If an idea is used in one episode, results of that idea will be used as well. For example, Ship in a Bottle had Dr Crusher running a full bioscan on Captain Picard towards the end. Imagine combining that with a basic monitoring program, so if the crew member's vitals go out of certain limits the crew member is beamed to sickbay, or at least some sort of alert is flashed.
Troubles caused by technology failures will result in better tech safety in the future. For example if there is a holodeck malfunction where people are trapped, then power cut-outs will be installed to force halt the holodeck so it does not happen again. Protective clothing will be worn in case of trouble, such as cooling leaks in Enginering.
Aliens will be played smart. For example in Voyager, the Maalon Captain would have agreed to share the antimaatter waste cleaning technology, but instead kept it for himself and used it to make much more money. When Voyager was put on trial, they would use actual examples of what Voyager had been doing to prove Voyager is a danger (such as Captain Janeway leaving the Vidiian base intact, making it look like she was working with the Vidiians to get more biosamples).
If a race is a major threat in the future, then they will be just as big if not bigger threat in the past. Enterprise's Regeneration episode would have been much scarier if 2-3 main characters had died, instead of Phlox being able to slowly fight off the assimilation nanites (now if the Borg had only managed to scratch him, and the crew had to keep amputating parts of Phlox's body to try and get rid of them, that would have been scary). To me, that episode should have had people tuning in because it looks like the entire series is going to end right there.
Aliens have their own plans, and in some cases all the ship can do is try to guide them, instead of stopping them. Sometimes guiding is not possible either, so all the ship can do is reduce any damage that will happen
One idea I had for a Star Trek RPG was set near the
Hekaras Corridor. The crew is sent there to chart the subspace rift that formed, measuring its expansion, and adjusting travel charts to adjust. Then a Borg Cube shows up. It scans the rift, and sendsa message to the PC ship to copy over all data the Starfleet ship has on the rift, along with a time limit. If they resist, the Borg ship defends itself, taking parts out of the PC ship (and replacement crew) while sending over drones to hack into the computers and get the data. After the data is gathered, and sufficient repair materials/crew is acquired, the Borg leave the Federation ship. he Borg ship deploys a sphere to continue scanning the rift, and after some time, the Borg ship sets a course for Hekaras II. Once it is within comms range of the planet it tells the planet to copy all data concerning the rift to the Borg ship (and a longer timeframe due to more data is expected). Attempts to use computer virii in the data will be unsuccessful. Once the Borg ship has the data (peacefully or not), it returns to the rift.
Back at the rift the Sphere is recalled, and the Borg cube stops its scanning. It then launches the Sphere again, but when the Sphere gets near the rift it separates into smaller components that surround the rift. The components shrink, and the PCs get to see the subspace rift shrinking as well. Soon the Sphere has returned to its original configuration, and the subspace rift is gone. This was never a Borg invasion. It was a road crew fixing a pothole.
