I agree with your summary. I think the Cyclops has grown on me with time.
It’s not perfect as a mobile base platform, but it is very much that. I’ve noticed I just grind time with more and more bases, so having to learn to lean on it as a base frees me from a lot of the later game grind. It’s really not good for anything on than slow speed, maybe medium if you know your safe. And all the extra additions for safety are really nothing when the biggest safety is turning the engine and lights off. The only hard part is navigating the damned thing down the river and through the woods to grandmother’s house. I tend to lay things out as such: in the small passageway between the command room and the mobile vehicle hatch I’ll put about 5-6 stand up lockers on each side, front to back, with the final wall on each side with 2 wall mount lockers. In the back of the command room I’ll put a modification station, a fabricator, a small battery charger, a health pack creator and maybe another locker or two. Initially I’ll have a few single plant pots between the mobile vehicle hatch and the cyclops loadout bays, but later those are replaced with large 2x2 planters. I also put one planter down below the hatch to leave the Cyclops, and I’ll use that to, “top up,” before leaving or as an emergency when coming back.
My only real need for a base late in the game are desalinization for water, if even, or a moonpool and subsequent vehicle mod station for upgrading the prawn if I’m unable to do it another way. At that point of the game, the Cyclops IS my base. Having to set up a real base is the pain.
To that end, my recommendations for anything related to a cyclops mod would be: Trim it down lengthwise. There is a lot of unused space on the rear and bottom of the sub. It would be so much better and more mobile if it were trimmed up just a touch. Allow more options to recharge it, as you stated. Allow it to have a mobile vehicle mod station. I mean it looks like it has one already, why isn’t that thing fully featured? Maybe as part of charging options, allow the player to build forward charging stations more easily. Say something like a thermal power generator and an attachment that does charging to vehicles within a sphere around it. This would let you still leverage the Cyclops as your FOB but also allow you to set up small charge areas along the way, wherever that may be. Nuclear in this game is mostly a waste of time. At the point of the game that you have what’s needed to use it, you’re well beyond even needing to set it up anywhere. I’ve yet to run through control rods at a single site I’ve used it, simply because you finish the game before they do. Yet, uranium is all over the place by the time you’re at the end of the game. Nuclear on the Cyclops, on the other hand, would be insanely convenient. Almost as if it may have been a part of the game, then someone took it out. Make it a challenge there and add some degree of inherent danger from it. Like modded minecraft reactors and balancing levels correctly under load to prevent issues. As it is now, it seems like the perfect marriage for the Cyclops, only unrealized.