With Trek, size of a star-ship is not a decisive factor.
Most of the things that matter in size when SF ships are concerned are the amount of materials, torpedoes and crews a ship can carry.
I mean sure, you will also have classes of ships on which size will be a decisive factor when it comes to how much raw power they will be able to churn out, but at the same time ... technology advances, and the reason why I can see SF building downsized versions of larger vessels that have same power output for example would be to bring up their fleet back on par as fast as possible, and be more prepared if combat situations arise.
Deus Ex machina aside, the Intrepid class is a sensible design.
Voyager was never stated to be a scout ship of any kind.
In fact, Neelix mentioned in one of the episodes when acting as an ambassador that one of the ship's functions is deep-space exploration.
Also, I fail to see why would it be impossible for the Intrepid to be on par with a Galaxy class when the Defiant has an impressive fire-power output at it's disposal while being far smaller.
I don't think SF would completely stop production of Galaxy class ships ... but I also don't think they would be in a hurry to construct as many as possible.
The Sovereign (despite it's combat capabilities) is still a large enough vessel that can easily fit into the roles of a Galaxy class ship as well, while being easier/faster to construct.
SF likely wanted a far more efficient all-round design that would be more combat capable after all.
Besides, I think the Dominion War prompted SF that they needed small, but much more powerful ships at their disposal that would be able to fit exploratory roles and still pack a punch.
Obviously the Defiant class ships can be used for border patrols much more effectively instead of sending an Intrepid or a Galaxy that could be much more useful in exploratory department.
Prometheus ... primarily combat oriented design for deep space tactical missions (as stated in the episode) obviously with same offensive/defensive capabilities of a Sovereign class ... yet being MUCH smaller (even smaller than the Intrepid if I'm not mistaken).