A REDACTED battleship with an alpha core integrated is the second most powerful ship in the game (below singing friend encounter 1 and above REDACTED 2: Electric Boogaloo). Operating at 45% combat readiness doesn't even figure into that. The larger issue with the automated ship skill is that that is the best use of it and it makes every other recoverable automated ship redundant once you can get your hands on one.
Automated ships skill gives you free officered ships. Meaning free ECM and some other stuff. A lot of it actually.
I agree on the [REDACTED] battleship making all other [REDACTED] ships essentially worthless if you can get your hands on one, I feel like that needs to be tuned now that the player can have them all in their fleet rather than just being NPC-only ships. There should be some amount of decision-making involved in what [REDACTED] ships to keep and field based on your play style to make it interesting (like picking regular Sector ships for your personal fleet and to fly), rather than always being "[REDACTED] battleship + Alpha Core".
I disagree with the implication that Automated Ships is already overpowered or fine where it is. Given that it's at the end of the skill tree requiring 5 points of investment (1/3 of your skill points), it should be powerful; and it should also be a similar power level to the huge increase in combat power of potentially giving every ship in your fleet a free extra built-in hullmod plus more max vents (and capacitors). By contrast, even if [REDACTED] ships individually are more powerful than their Sector counterparts (debatable, at least for anything other than the battleship) they are not "free" and can't be made better by using story points: they still take a slot in your fleet, the still cost maintenance/fuel etc, they still cost DP to deploy in battle, and on top of that unless you have an extremely limited number of them (30 DP or less, which is one cruiser with a Gamma Core) they'll have such low CR that at least their accuracy will be affected or they could have a risk of malfunctions even at their max CR.
If we could spend a story point to add a special hullmod to them individually which has to be built-in and adds another +30% CR for automated ships (which maybe costs more than 1 story point for ships larger than frigates), at the very least, I would consider it on-par with Special Modifications. Right now, power level aside, I don't consider the Automated Ships skill to be rewarding for the investment beyond the (brief) initial novelty.
I feel like Zaizai summed it up really well:
One choice is to make my whole fleet stronger, doubling the vents on frigates [or easing flux pressure on flux-hungry capital ships], adding otherwise extremely costly hullmod to capital ships [for just the cost of a story point] etc; the other is to get a single strong ship that i can't even use as flagship [or maybe one or two cruisers] and has lower cr than the rest of the fleet [to the point where it has accuracy and other debuffs or suffers risk of malfunction while at max CR].