To paraphrase one of the technology blurbs in the game:
Space is big... really big.
Even in the realively modest confines of a solar system, a non-hyperdrive ship is going to have a hard time delivering its impressive package of weaponry if it is in orbit around Earth and an enemy ship pops in out of hyperspace, say, at just halfway between the orbits of Earth and Mars. That non-hyperdrive ship could start steaming its way to the offending ship and would get there at sub-light speeds in about, oh, 3 months or so. The Terran captain decides that would be futile so it's best to stick close to the planet and and defend from there. The attacking ship then vanishes just to reappear moments later at Earth's doorstep, at about the orbit of the moon on the opposite side of planet as our intrepid defendor ship. Hmmmm... thinks the captain, should we start working our way around the planet to put ourselves between the attackers and Earth? Why not. Full steam ahead. We'll be there in less than an hour, two hours, tops. I'm sure the enemy will be there waiting for us, unless they are in a hurry to invade our planet or something crazy like that.
Consider, though, just how powerful one of those ships would be in it's defensive role. You can circle a planet in a few hours if you're using a low enough orbit, and the races of GalCiv obviously have some kind of superluminal sensor that lets them see incoming ships from a distance, so you would have forewarning.
Consider then that the hull size limitations that most ships have to deal with are the fault of the hyperdrive technology... larger ships break apart in warp fields unless properly compensated for. A ship that does not enter hyperspace is then free to be as big as you want it to be... the size of the ship is not a significant issue except in terms of thrusting.
Now, you'd want to put a reasonable cap on the size of them. For one, being able to thrust the ship around is an excellent defensive measure... a good random walk can make it very hard to target and hit you with weapons that travel at light speed or slower. A ship that can't accelerate fast (like starbases) would be following a completely ballistic path, making it rather easy to smash a rock into you from any old arbitrary distance. You know where they'll be.
That isn't simulated in the game, though (or maybe it's the reason starbases are so limited in hit points...). However, you've got to admit that defensive orbiting stations loaded with your latest military tech (and without needing pesky engines and life support!) would be able to provide a significant barrier to any would be invader... more so than orbiting fleets would!
I like econundrum's solution, which is pretty elegant. The downside comes in the form of the updates needed for the AI... they'd need to learn to put engines on all their warships. It'd also mean a significant speed increase across the board, once higher level engines are unlocked. If engines are mandatory, and you just happen to have warp drives... thats 3 movement right there, without even considering the +speed abilities that are built in by default now. Then again... Frogboy's been talking about revamping the AI anyways, so maybe this is just the time!