I sometimes wonder if these Berlanti shows are so indebted to the Buffy formula of having a new Big Bad from the start of every season, that they commit to one without thinking it through all the way and then just have to half-ass it when it comes time to start tying things together. Maybe they should go back a step and just do more of a 90's style villain of the week type of show, but keep focusing instead on the character relationships, and then bring in the villain with his fully formed plan halfway through the season instead.
Before that you could maybe build him up with occasional, little scenes that show him doing or planning something that we don't get to see yet, but that the group doesn't know about at all. Honestly, that was kind of the way Reverse Flash worked last season, since Wells was fully part of the team as far as they knew, until about halfway in.
And I think that worked better because it allowed the show and Barry specifically, to have that light, fun, happy go lucky kind of feeling instead of keeping him in the dumps this entire year. The lightness was the charm of the show that people praised, and his adorable puppy dog attitude that's been missing this whole season.
And Buffy didn't always have the Scooby gang know about the Big Bad from the beginning either- for example, Angel didn't emerge as Season 2's villain until the second half, and while the Mayor was established in Season 3, they didn't become aware of his evilness until later on.
I just think setting up Zoom as the villain they're all aware of from the very beginning has really made it seem like a drag on this season when he kept showing up and then disappearing, but they had to keep talking about him anyway. I know the 23 episode season is a struggle, but I think structuring your villain story to maybe not ramp up until the second half, and then just devoting the rest to great individual episodes (while keeping the focus on continuity by developing the characters you have, like for example Caitlin and Cisco, or even having different characters interact with each other and not just Barry) will help sustain the show overall.
I also think they just really need to bring Happy Barry back somehow for the next season, because that really was one of the most appealing, key parts of the show (the contrast between "sunny" Central City and Arrow) and they've kind of let that go this year, which I think was a big mistake.