Hostile Waters does use scripted gameplay as well, but unlike Seamist it does so with balanced teams and more traditional base layouts.
The reason you don't see too many of these maps is because it takes a while to set up (Hostile Waters using about 40 or so scripts for the end game logic, not counting the bonus objective scripting).
Back between Beta and Gamma, the APB dev team was tossing around the idea of making most maps have some objective of sorts, or at least a more clear plot. This never became reality due to various reasons.
I personally still think that each map should have something more unique to it, to help make gameplay more varied. This way Zama and Bonsai don't end up playing more or less exactly the same like they currently do, and it allows maps to play differently not exclusively by their layout alone. The problem is you can't just add objectoves or bonus objectives to every map and have it make sense... The maps need to be designed with it in mind, or greatly modified.
In truth, possibilities would greatly improve if we had an additional in-game resource besides credits, with different uses, and possibly map-specific. Right now everything is tied to one resource, or existing building functionality.
Edit: Expanding on that idea, if we had a new resource pool (let's just call it "Resources" so it becomes more general-purpose), and have this resource be team-shared and not unique per player like credits, then you could have teams work towards building up a pool of "Resources" from map-specific objectives (securing and holding a lumber yard on The Woods Today, holding a warehouse on Metro, etc.), and then a team member could spend these resources on a special terminal to activate a team buff, purchase a special unit, upgrade buildings (gain interior defenses), or build additional structures... You name it. By not tying this or map objectives to the regular credit-based economy, you don't mess up regular gameplay balance, but still achieve interesting results that can spice up map gameplay variation. If enough upgrade options exist, then a sub-game of technology racing is added to the game, to make sure your team has more things unlocked.