I think your modules ans some other things could be improved.
The main things you should focus on are:
More firepower: Remove some electrobolts and replace them with some more damaging weapons.
Improved supply: I see you use modules, which is great. Yet your modules could be much more effective. Try to match the amount of cannons with the amount of factories: 1 factory = 1 Large cannon or 2-4 small cannons, (depending on if you want them to fire non-stop). Move your reactors so they touch the shields, (1 reactor for 1-2 shields). Your ion beams also need a better power supply (also, one lacks doors).
Minor things you should take a look at:
Missile modules: Right now your missiles and engines are supplied by the same crew, make missiles independent for a much better missile rate and better thruster powering.
Control room placement. Right now your two control rooms are as good as one, since they sit next to the same reactor. A tactical shot takes out both. Move them to different places, and make sure it's difficult to take out both.
Try improving your combat against these two. You don't need to beat them yet, just make sure to get that damage up!