Desilu had a huge overhead charge that ate up a lot of budget, but was that overhead carried over when Paramount took over?
With less overhead, they might have had MORE of the budget actually available to use for the actual production 3rd season, which would explain how they could drop 90 grand on just the vfx for THOLIAN (that is the figure Mike Minor was quoted as citing when interviewed about his career in ENTERPRISE INCIDENTS magazine. Occasionally I wondered if it was a typo, but 9 grand sounds way low, even for back then, given that it was something like a three month stint to put that stuff together for the episode.)
Also you've got rear projection on the bridge a few times, which, while it saves on opticals, costs in stage time to set up. And great bits like the aforementioned obelisk (which must have been built solid, because it would have been blowing in the breeze if it was a lightweight construct) and the klingon cruiser - especially that nice bit of animation when it gets vaporized into milk in DOVE.