Alright, having had a chance to play around with it now, I believe I'll implement the following changes to ships:
Charybdis: Flux increased from 10,000 to 12,000, and vents from 550 to 700. Ordnance Points increased from 125 to 135.
Morningstar: Flux increased from 5,500 to 6,000, and vents from 350 to 400. New Standard variant added: Heavy Blaster, 3x Tac Laser, 2x PD Laser, 2x Harpoon. Old standard is now Anti-Flux variant.
On the subject of the two missions:
Out of Your Depth seems largely fine, particularly with the new changes to the Morningstar. The only planned changed is increasing available Fleet Points; it is important to remember that this is an escape mission, and defeating the enemy conventionally is not the plan. Bloodying their nose, however...
The Bender's problems could not be resolved by buffing the Charybdis, rather it's a legacy (and laziness) problem - balance changes 0.50a (when the mission was first authored) and 0.52.1a (now) have changed the Balanced variant of the Eagle from a difficult but still defeatable opponent to an
absurd Charybdis wrecking machine, capable of completely overwhelming its flux capacitors and punching through it's thin armor from completely outside the Carrier's range. The laziness comes in from my pre-release testing; I played through the mission and managed to tweak the AI and get it to retreat... without seeing what the Eagle was capable of. Switching the Eagle over to the Assault variant made things easier... to the point of being genuinely easy, rather than the difficult but passable challenge I was going for. More thought is required.
Other possible changes:
The Skinwalker is perhaps underpowered, due largely to not shooting enough. Considering replacing Burst PD with an I.R. Pulse Laser or (to be ridiculous) medium Pulse Laser.
The Morningstar likely has too many Ordnance Points. A reduction may be called for, from 80 to 70, considering I'm able to fit two to three hull mods consistently and 15 to 20 points in capacitors and vents.
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How dare you!
Personaly I like the color scheme, would like to see a full faction in this theme. Sure, i can imagine it would be more "mainstream" if they were made form the red/dark red + gray, black combo or blue color, but they fit perfectly in the game visualy. I would personly add more of the brighter green/cyan on several spots on the ship, but by no means I would call this ugly. 
Hehe, no need for vindiction. More of the brighter green/cyan? Not quite sure where I would put it, but I'll keep it in mind. In any case, I'm glad you like my work, and...
So yeah I will use the most generic response there is - moar of this! Then will see how it develops + more ships of this design will make you love it eventually 
I shall do my best,
Mon Capitan!Edit - just to make sure, if it wasnt clear - everyone can express their oppions, right ? I think its both constructive and usefull(given that theres a reason why added to it, which it was), the way i reacted.. is just the way i am, nothing offensive 
Aye, and frankly it's expected that some people won't like it for whatever reasons. It's fine, those are their reasons, and they are welcome to them.