Remnant frigate spam is a thing because cores count as officers for now, which they will not for the player next release, so that use by late-game goes out the window. I suppose player can get Auto Ships to use a bunch of AI frigates during early-mid game as a crutch.
I would not worry about Gauss cannons on Guardian. Gauss is slow and not very effective against a group of small nimble targets. 900 range ballistics is more reasonable.
Paragon is not as good as it used to be. It still has the firepower, but its defenses seem weaker despite being unchanged from before.
Radiant is a monster. It is the only thing that makes Automated Ships worth taking instead of Special Modifications by the end of the game. Of course, its competition will be Neural Link, which looks lackluster if not for its ability to pilot automated ships.
See, this is the problem. Guardian IS indeed so good you have to get it, even without missiles. If anything, my argument would be the opposite. You really want your OP godship - make a mod for it.
Unskilled Guardian does not seem much stronger, if at all, compared to Radiant in a brawl. It has the mobility to run from corner to corner and lob unlimited missiles, which is rather degenerate. (Enemy ships tend to avoid the corner.) Strip unlimited missiles and it needs get in there and brawl. Of course, that assumes both Automated Ships and Neural Link for player piloting. If not for Neural Link, Guardian would be fine because AI would not exploit its advantages to the fullest. Maybe Guardian can be made much better with skills, but player who wants to pilot it will only have seven skill points left for the other three trees. Will that be enough compared to someone who goes for other top skills instead of the Auto Ship and Link combo?
And part of the point of getting Automated Ships is exotic (mildly) overpowered ships because player is giving up better skills for it. If the only point of taking Automated Ships is to play as Ash Ketchum and collect more ships that are no better than human ships for your ship collection, then the skill is suboptimal at best and useless at worst. Well, I guess someone can get Automated Ships and one of the top Industry skills for a live-off-the-land playthrough.