I went a different route and banned all Ph-2 from combat ships (except for fighters) which meant an instant upgrade to many older Klingon, Hydran and Lyran ships. Only civilians, freighters and an occasional pirate have Ph-2's now.
I also redefined drone control to be a factor of not only whether the ship is a drone boat, but how many racks you have on the ship, with Mirak having an advantage (i.e. able to control more drones per rack than other races) to make up for the loss of all the drone types that didn't make it into the game. I've also given Klingon carriers drone racks.
I need three shiplists because I have outfitted all the carriers and other fighter bearing ships with era current fighters right out of space dock. If you'll notice, fighters are classed into four types: Patrol, Interceptor, Heavy and Assault. Based on the role of the ship and the number of squadrons, I choose appropriate classed fighters for the ship. For example, as a human player I'm likely to fill my fighter bays with all Heavy or Assault fighters, but an AI ship (say a true carrier with 4 squads) will have 1 Patrol squad, 1 Interceptor squad, 1 Heavy squad and 1 Assault squad. It makes fighting the AI about 100% more interesting. At the right times I swap out the shiplist and all the carriers a have new toys.
I decided to use the Phaser-A as a scout channel. It is the only thing in the game that even resembles the jamming capability of scout channels (by having that "stun" effect on bare hull). It gives scouts an actual role and I have a whole strategic layer devoted to them (out of five). The number of "scout channels" a ship can have is severely limited.
I've improved Def-Sats, given Klingon command ships better dizzy firing arcs, improved asteroid bases, reworked release dates for tech, redid the fighter weapons loadouts, added monsters (and pregnant monsters) and am in the process of reworking many power curves on some of the real dog ships, reevaluating the power curve needed to use the cloak effectively, restricting Taldrens X2 ships and using their tech more effectively. I'm also going through and deleting all the extra junk in the shiplist we don't need and reworking others to use the right UI (I like my Tac-Intel correct).
Your Breen idea is unconventional. You're trading out a fast firing, free holding range of effect weapon for a slower, constant power draw to hit/damage weapon, that does less damage overall. And they seem to have no PD.