The "Elite Units" (units that take up the cap ship slots) are the "Hero" units of the mod. Not all of them are "true" capital ships. The Defiant we consider a hero unit. Just like we consider the Sovereign despite her size. The Elite Units stand way above the standard rank, and file cannon fodder units like the Intrepid. Voyager was a standard light exploration cruiser stuck in a very bad situation, and miraculously pulled through it (through the help of some very inept writing that we wont go into). In other words.. Voyager was an exception. Not the rule.
The reason why ships became Elite Units, and we made the Elite Units this way is mainly for Balancing purposes. So that very powerful ships are limited in their numbers, and are very expensive to research/build. On top of that there are not enough Cap ship slots to represent all of the ships that should be "elite". So we made some tough choices that not everyone would like.
The Defiant packs damn near the fire power, and shield/hull strength of a Galaxy class crammed into a small highly maneuverable hull. It was in the Heavy Cruiser slot before the Intrepid was, but that proved to be disastrous when the AI would build hundreds of them. Hence game over for the Borg, and any other faction! The Intrepid class was honored by it being in the "Heavy Cruiser" slot (where both the Defiant, and the Akira were once before), and she is one of the most powerful of the non-elite units, because of her "Anti-Borg" ability's. We dont hate on the Intrepid itself (as its position in the mod proves). We just hate the show it came from.
You will see other "cruiser sized, and under" ships in the elite slots of the other factions. The Dominion has the Keldon which is just a modified Galor class. However it packs much more firepower, and has abilities that keeps the Cardassian units "in line" (prevents their mutiny from the Dominion). The Harbinger is a cruiser sized ship as well.
The Romulans have the Z-1 Nova, the Melak Warbird, and the D'Verix Warbird which are all below "capital ship" size (at least from the romulans point of view).
The Klingons have the K'Vek, and the Vod'Leigh, and now the Kron. All well below capital ship size.
The Borg have the Queens Diamond. Definitely a tiny ship compared to a cube.
There is madness to our method... err.. i mean a method to our madness 