Well, I think the intention of the designers was that the saucer would normally be left behind in a safe place before the battle section went off to a military engagement. Or, as we saw in "The Arsenal of Freedom," if the ship came under attack, they would retreat to a safe place, separate the hulls, and then take the battle section back to engage the enemy. The situation in "Encounter at Farpoint" was presumably meant to be somewhat anomalous because the ship was unable to retreat from the threat and had no choice but to separate the saucer during pursuit and hope it would be left alone. I imagine that if the miniature with the separating hulls had been easier to work with and the producers had used it more regularly, you might've seen more episodes opening with something like, "Captain's Log, stardate 42424.2. The Enterprise has been ordered to investigate a possible border incursion by the Meanalien Conglomerate. Thus, we are leaving the saucer section behind at Starbase 23-Skidoo and will proceed to the border in the battle section." Heck, they even could've done an A-plot with the battle section engaging the bad guys and a more character-driven or comic-relief B-plot back aboard the saucer. You have a point, though; it would've made more sense if maybe both hulls had had warp capability. I guess they didn't go with that because it would've been too great a departure from the familiar saucer-and-two-nacelles design.