Damaged fighters go to a carrier for repairs on their own, there's hardly any micromanagement necessary. True, they die quite easily (and that's annoying), but that's nothing you can change with MM.
With your idea low CR becomes much more critical for a wing than the damage it suffered. Suddenly micromanagement is very necessary to keep it alive, even though, as you said, its overall survivability has increased by leaps and bounds.
I think I'm assuming you play similarly to me, which may not be the case. Also, "micro" may have been a poor choice of words.
So, every now and then I pause and look at the map to make sure my other ships aren't doing anything dumb or getting overwhelmed. If they've started taking hull damage or it's simply too risky to have them in a certain area, I order them to another part of the map or retreat them (the "micro" I'm referring to). Other than that, I leave them to do their own thing. My micro can be summed up as "go over here so you don't die horribly."
You don't like that fighters can die quite easily, as do I, but that's something that micromanagement CAN help with; it just requires a disproportionate amount of effort compared to microing a frigate since frigates don't die as quickly and are less suicidal. Still occasionally have suicidal whims, but less than fighters. Once again, 'micro' refers to telling them to gtfo.
I think the main difference in our opinions is due to how the potential changes wouldn't affect my playstyle at all while making fighters a worthwhile investment for me, while it would make you look at the map more to use fighters optimally, I'm guessing?
With your idea low CR becomes much more critical for a wing than the damage it suffered.
...
Imagine you have a fighter wing engaging an superior enemy. Two things can be the case:
They have high CR and their destruction doesn't matter much.
Or they have low CR and their destruction is permanent.
Those two situations are very different (as much as a current full HP wing vs. a single surviving fighter with low HP), but they look exactly the same on the combat screen. Evil trap.
I agree that it makes CR more important for fighters than their health bar, but I don't see that as a problem. Here's how I envisage your scenario would play out, for me anyway-
You have a fighter wing engaging an enemy and it gets destroyed.
Case 1: The fighters have high CR. Their destruction means they will be less effective when they return (remember CR replaces crew's combat bonuses).
Case 2: The fighters have low CR. Their destruction means they're even less effective. They may have to sit out the next fight as well. Keeping them deployed risks permanent destruction.
Case 3: The fighters have basically no CR. Their destruction is permanent.
The risk gradually increases while the effectiveness gradually decreases. The key thing is Case 2. Case 2 is where you get to make a choice, the choice that you normally don't get to make currently- the choice to retreat the fighters. I think that's incredibly valuable, even if it means CR becomes more important than their health bar.
I also agree that it should be easy to tell at a glance how high a ship's CR is. I'd actually like to be able to see the status of all my deployed ships on the combat screen so I don't have to keep checking the map. Perhaps a row or two of little pictures of your ships with their armor status, each with a little bar for their flux level (no need for numbers- its enough just knowing how full the bar is) and a little bar for their hull integrity, as well as their %CR somewhere nearby. I'm imagining something along the lines of what MMORPGs use to show the status of your party members.
EDIT: If it helps, you can just check your fighter's CR anytime you read the message that they've taken off from a carrier. That seems like the simplest point to make your decision to retreat them or not ...assuming the next build goes the way I think it will.
Ooo, idea- anytime a fighter wing is destroyed or takes off from a carrier, the message that appears could contain its %CR.
Example: "Broadsword Wing (37%CR) takes off from [carrier]."