I just read a fascinating article on Popular Mechanics entitled 8 Sci Fi Writers Pitch Their Dream Star Trek Show. Some of them are great. Others, not so much. But I thought one up myself, and I'd like to share.
Similar to Mur Lafferty, whose podcast fiction I'd listened to years ago, I'm fascinated with the possibilities of transporter and replicator technology. When weaponized, I can imagine these two technologies making phasers and photon torpedoes irrelevant. A ship dedicated to transporters could easily have hundreds of transporter units. This ship could threaten fleets or even entire planets by threatening to kill or capture thousands of people by simply locking onto them with transporters and then intentionally losing the signal, or just dropping them into a cell. You could lock into an entire room of people, kill a dozen, capture a dozen, and leave three of them alone.
Of course, the issue with this inside the Trek universe is shields. I'd imagine that only militarized vessels would have shields, but shields do certainly stop the transporter shenanigans completely. So if you're planning on doing battle with the big boys, you need some way to bring the shields down. You could design your whole ship without any destructive weaponry. Only some kind of beam (I think the Borg had this) which does nothing but drain shields. Once the shields are down, you own the other ship. Design this transporter dreadnought ship with large cells, then the other side won't want to destroy you for fear of killing their own mans.
Another option for getting around the shields is to explore ways to exploit the shield frequency vulnerability. Maybe it's just because I'm so technically-minded, but this type of security research stuff would be fascinating as an element of a Star Trek show.
For nonstandard defenses, this transporter dreadnought could beam large amounts of material into space to block line of sight between itself and the attacking ship. Stuff which would cause fired torpedoes to explode early and deflect phaser fire. I'm sure that research scientists who knew exactly what a phaser is (I don't) could come up with some kind of ideally suited thing which has a minimum of mass and maximum effect.
This isn't really a story - more an element that can be used in an episode for an interesting and nonstandard adversary. I'm signing off now, so as to not fall down the Star Trek technology rabbithole.