I've only read through the OP, and I disagree. If kiting is how you want to play it, sure, but I just see it as this:
soloing is basically just exploiting the ai's slightly deficient force-estimation capabilities and the current absurdly powerful nature of player skills. i don't think it should be catered to. it's a fleet combat game dammit.
CR, deployment costs etc. help link together the context of each tactical battle with overall "strategy". In its current form I love it, probably wouldn't enjoy the game as much without it.
That's not to say there's no room for improvement - CR encompasses both how well the ships' systems are maintained, and the morale and ability of their crews - I'd prefer to see those separated, with crew experience defining the flat rate of CR degradation and its cap, with morale as a modifier. The more experienced the crew, the less both positive and negative events influence their morale and therefore the more stable their ship's CR is. Backing away from the battle would allow their morale and therefore the ship's CR to recover, the rate of CR recovery being defined by morale and experience. The ship taking hull damage during battle would reduce its maximum CR throughout the battle, while crew deaths would do the same for morale.
What's behind idea is this: The stress on both crew and the ship's systems isn't uniform throughout the course of a battle. The chance of malfunctions and overall performance should be more influenced by events (Damage, crew death) than time. If you haemorrhage 80% of your crew during a fight, the enemy don't even need to cause any more damage because the remaining crew will be stretched thin across its systems, in addition to being less efficient because of the demoralisation caused by their buddies dying. If you've been in a knife-fight for an hour straight, the ship's systems will be under constant stress and will mechanically fail from time to time, but if you've been scoring victories throughout, your crew will stay on top of it, especially if this is their 100th battle. So in other words, if you're fighting conservatively you can maintain CR indefinitely, and if you're being reckless and aggressive, or biting off more than you can proverbially chew, you will expend CR depending on your crew's experience, size and morale.
Couple "little" things that'd have to be changed/added - Rather than CR having thresholds for malfunction chances, those chances would scale dynamically with CR. Even at 99% you might lose an engine for a few seconds, but it'd be extremely unlikely and fixed quickly.
You'd also have to be able to assign the crew of a ship, ie filling your best ships with as many elites as you have, then veteran, etc relegating your least experienced crew to non-combat ships for example.
You should also be able to prioritise which systems your crew will work on, for example if I set engines at high priority and most of my weapons low, engine malfunctions will be less likely and fixed quicker while the inverse is true for those weapons.
I might make a more detailed post about this proposed system later because I haven't really got it all sorted out in my head yet, nor did I really articulate it well.
Oh, since phase ships have been mentioned - I bloody hate the things, it feels like the only time I can get a clean kill on them is if the AI makes a mistake.
