Apogee is slow and short ranged ...
Hammerhead can defeat it in completely ...
Tachyon + 2 Tactical lasers lasers + ITU + Adv. Optics = Gives about 1600 range. (feel free count exact number include pilot bonuses) Thanks to Tachyon "pulse" beam delivers damage over short time period, without need long time target aim.
add (Squall+ Breach) linked + missile rack = enough rockets for anything
Pilot : Missile Specialist elite, Field Modulation elite, Gunnery Implants, some other skill,
If you can still encircle somehow with Hammerhead, then I can add Thrusters Hullmod for better turning, so you cant.
I sold Apogee in my first playthru, because It looked like too expensive and doing nothing. When you mount Annihilator to the weird positioned small slot, it makes ship dance like madman. Well, after some time I learnt to read rocket desc. :-] Now, I see, it is actually one of the most useful ships. When you find proper weapons and pilots it offer perfect price to performance ratio.
Definitely prefer Apogee over Eagle or Falcon.
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Mr. Alex,
could you post the upcoming patch notes sneak peak? Specifically the balance part, so forums addicts gets some snack in advance.
Pour some fuel to dimming fireplace. 
Thank you