I absolutely love that you can do it both ways, and playing like an rts can also give you another advantage in that you can pause to think about things, playing in the action, or another RTS you can't do that. And being able to pause the game and think about the action can let you figure things out, "oh my lasher over here is in trouble it seems an enemy fighter wing broke it's assault on my venture and is kicking the crap out of it, well i'll have to retreat that, *being paused you take another moment to look around first* oh well wait i have a wolf nearby that i can send to assist it and make absolutely sure my lasher doesn't die" This exact scenario played out the other day for me, and im pretty sure without that wolf's support the Lasher would have died, granted a lasher isn't that important in the grand scheme but i'd rather have it's 5 guns and harpoon racks at my side than not have them.
Also i'm partial to playing in both ways, in that i pilot our large kick-ass flagship ( usually a venture or onslaught) and pause roughly every 30 seconds, or if i see something going on, just to check on the fleet, and i also issue orders to fix situations like the one above or to do other important things.