STO could learn a lot from the Starfleet Command series, even if there are some inconsolable differences in terms of gameplay between the two. Just because you have complexity, doesn't mean you have to increase difficulty. You can have mechanics in place for distributing power between beam weapons (just as an example) without having to expose this to casual players. Like pealing layers of an onion players can delve as far or as little into the mechanics as they wish, assuming the more advanced mechanics are not expressly required to play and succeed at the game.
what would really be nice (as an addendum to OP's idea) would be weapons with different arcs a la SFC. Rather than having simply front and rear-mounted weapons, have the hardpoints either distributed around the ship (fore, rear, ventral, dorsal, etc) or with players the option to rotate thier firing arcs (leave beam arrays with a 250 degree arc, but allow the player to decide which direction that arc faces).
Wish Cryptic would implement more ideas from SFC3. I liked how instead of ships varying in performance, performance was based on your gear. Like the more weapons, the slower and less manuverable you were.
Perhaps Cryptic would implement different types of beams, like shorter weaker beams with higher firing rates or slower beams with longer reaches.