Gemini was a fantastic little hotrod of a spaceship.My personal pet theory has always been that it was a precurser testbed for the NX-01 technology. Like the real-life Gemini capsule was already halfway a ship from the Apollo mission, technology-wise. T
The Intrepid version of Gemini might have been this alternative design that could have been used instead of Apollo for some missions. Meet "Big Gemini", ugly duckling extraordinaire with seating for 10:

(I love these oddball might-have-beens)
I like these kinds of discussions. its fun to speculate. Dierdre as a drone cargo ship like those cargo craft in TAS makes sense yes. At least 20 years ago there were still dhow's in the Indian ocean and Persian gulf working commercially so who knows, maybe those warp 2 crews are jsut really traditional....although, for all we know, she and her convoy were unmanned robot drones like the Woden from "The Ultimate Computer" (TOS) and those from "More Tribbles, More Troubles" (TAS)—and presumably those which visited the similarly automated lithium cracking station on Delta Vega only once every twenty years per "Where No Man Has Gone Before" (TOS)—with only a lonely maintenance engineer putatively "commanding" her at that moment to send the alleged distress call! ("Babel" [DS9] saw O'Brien musing about such a posting a century further on, too.)
At any rate, "Fortunate Son" (ENT) itself did show us that among cargo haulers, some were quite content with the idea of retaining their tried-and-true Warp Two engines, even if others feared they would need at least a Warp Three one to keep afloat in the oncoming Warp Five era. But my point was merely that the option was apparently available to them. Personally, it's harder for me to envision forward-thinking Starfleet choosing not to take advantage of such an option in newly-built vessels than it is to imagine them electing not to refit outdated ships with faster engines they weren't designed for, or indeed doing exactly the latter, but this process being an undertaking requiring years to carry out. However, I do concede that there could be "reasons" for the first scenario, and further that the point becomes entirely moot if we simply ignore the script's suggestion of the Intrepid as being a Warp Two vessel altogether.
Early Starfleet purposefully building a Warp 2 ship could also just be taken as a show of conservative military thought. The US Army had seen and used reloading breechloading rifles since the late 1830s, and in the Civil War especially saw how effective Henry and Spencer rifles could be. They had a chance to build on that but instead just took the old rifle-muskets they had made hundreds of thousands of at Springfield, and did the Allin Conversion on them, turning them into what is now called the Trapdoor Springfield, and oddball ugly duckling weapon that somehow got used in active service for the next 40 years while the rest of the world moved on.