Besides, bigger problem would be command point shortage anyways. Command points are already so scarce yet so negligible in their positive effects (outside of most generic order of 'capture nav point A') that I am already encouraged to ignore command point system and to simply outfit AI ships to be more defensive so that they can just brute force their way out of the idiocy they sometime dwell in.
If frigates were to become this liability that require a command point per single frigate or else put my elite pilots in jeopardy, I imagine I for one would simply stop using frigates because it's already hard enough to justify frigates once cruisers come into play (outside of hyperion flagship).
Or take this approach... if players are suppose to order retreat to frigates/ships with low CR... shouldn't us players already be keeping an eye out for CR on all of our ships? So where would this extra burden come from if retreat were to cost CR instead of command point? You mentioned something about optimal order but I don't see how the optimal timing for retreat change because of the resource change since the cause/trigger for retreat remains identical (low CR).
What I mean by "optimal" is "optimal play". If retreat orders are unlimited, then "optimal play" requires you to order retreats for damaged ships at precisely the right moments, and to do that, you'd have to constantly watch the map. If it requries a command point, though, you're going to batch up orders anyway, so when you decide to give some orders, you'll also look around for whatever makes sense to retreat, and do it then. So it's a mode of interaction that doesn't intrude on the piloting portion of the game as much.
I hope that makes sense. In the early versions of the game, you had completely unlimited orders... which made microing everything as much as possible "optimal". That just doesn't let you focus on the piloting nearly enough. Given how that worked out (or, rather, didn't), I'm extremely wary of allowing unlimited orders for anything.
Could we get, instead, some generic fleet-level orders? Here are some examples of things I'd like to be able to do:
1: Have fighter squadrons automatically retreat if I have no carrier in play and they're damaged to the point where they'd normally automatically go repair.
2: Be able to adjust when fighter squadrons go to repair - in particular, I want two-fighter squadrons to be much more paranoid, heading for cover at around 60-75% total wing health+armor, instead of staying in combat when one fighter is down but the other is still untouched.
3: Have frigates automatically retreat at some specific CR level.
4: Have some special-purpose ships, like Buffalo IIs and Vigilances, retreat when they're out of LRMs.
This would give the player the ability to deal with things like ships needing to retreat at particular times, without having to micromanage the exact details. Add a combat status message when a ship decides it's time to retreat, and the player could go cancel the order (at the cost of a command point) if the situation really called for it. Or, y'know, they could just turn automatic retreat off if they didn't want it.
The above list just dealt with retreating, but there are some other things I'd like - for example, the ability to tell fighter squadrons to avoid capital ships, period, unless explicitly ordered to engage. I'd rather my wasp wings didn't get anywhere near an enemy onslaught, thanks.
...You may notice a theme to some of my suggestions, here. In general, I'd like to be able to fine-tune AI behaviors to better match what I want out of them; the same theme is behind my repeated suggestion of being able to adjust autofire targetting priorities. An ideal battle, for me, would be one where I come in, set a couple of capture commands, maybe deploy a few more ships once I have some nodes under my control, and otherwise spend the time flying my flagship and trusting that the rest of my fleet will do useful things on their own. I don't want to have to pay attention to CR levels of my frigates and give them even batch retreat commands. I don't want to have to pause, set my target to an individual enemy fighter, unpause, repeat, just so my phase beam turrets will actually kill off fighters instead of the destroyer I'm busily firing my plasma cannon at. Etc.