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Plainly speaking, an S class with the best upgrades will always have better stats than an A class with the same upgrades. Inventory is not the stat you should be wary of when upgrading since, as I stated before, you can upgrade ship inventory quite easily.
However since Origins the class will limit how many additional slots you can install, so S-Classes are getting better now.
I'm about to test this, and I almost can say yes, but I cannot yet define a rule. For freighters this seems to apply as well. I need to continue testing, something has changed for sure.
More feedback about it is welcome: Get a C-Class and try to apply your free augmentations, you should not be able to go up to 48 with all ship types (but which ones?). With S-Class of the same ship you should instead; because S-Class are now very hard to encounter - even in wealthy systems - this testing can take a while...
S classes typically are the best...but not always.
All ships and items have a random chance to have differing stats thus you can get S class things that just plain are horrible or lower rated things like A or B or C that are higher then your S rated items or ships.
To examples of this....I have S class mods..that increase my ship shield by 30% this is typical....i have an A class mod for shields though on one ship that gives it a 32% increase. I also have gotten an S class shield mod that was less then 30%.
On my living ships which are all S class...i noticed the base stats are random on each one.
And speaking of random....on a mission to hatch another living ship....instead of a living ship it gave me a crashed ship of the my original ship...thought that was kind of funny.
Another interesting thing....I found a A class frigate that was Huge.....on the outside it was massively bigger then anything else I had ever run into....i ended up replacing it with a S class due to how it had more internal inventory space from Modifications but it was not nearly as big.
I should have kept that A class as it was bigger then most system star bases and had way more stuff on its outside....too bad it would never be able to use all those turrets.
Right now ships are about the same as a cardboard box , throw some paint and decals on a box and u are real close the the ships u have in game...
Be aware that the game was designed for C class ships/tools. They have not really updated anything so once you have anything above C class, you are OP.
Now that you can make any ship an S class...with enough credits and nanites, the only advantage to finding one is saving some nanites. Their base stat is going be higher than a similar craft at a lower class (base level). They can have the most slots, even if they start out small...like the exotics.
The not very secret secret is that you need something to spend credits and nanites on. That is why they exist. If they only had C class ships and no way to increases the slots...you would be swimming in credits and nanites before you even got past the tutorial.
The attraction is partly bragging rights / completionist -- "Ive played for 5 years and have a fully upgraded S class ship of each type".
People play differently. A 40+ slot hauler C-class used as extra portable storage container is not improved by being S class (It may start with a couple more slots but you can find free upgrades to that over time).
The biggest advantages to S class really are combat related, or possibly warp drive range if you are trying to go to the center the hard way.
the same is true for S class multitool, freighter, etc. Its the best, but the game does not require it. The only thing I would argue as required to be S class are your tech install mod cards. Those are only 550 or so nanites, and even a beginner can afford one or two per space station visit.
While it has been shown that most S class spawns will have better base stats than most A class ships upgraded to S class, this is not always the case. I have found that there is usually an A class spawn that is better than all other A class spawns of the type of ship in that particular seed. Those A class spawns when upgraded to S class will be very close to the best S class spawn and better than many of the S class spawns of the same ship in the same seed.
So here's my strategy when I find a ship I really like: First, advice is to always look in a three star system. Second, once I find a ship I really like (looks of course), I camp the trade post and watch. When an A class spawn comes along, I buy it (or trade for it). Next, while still looking for the S class spawn, I check every A class that comes in. I keep trading up my A class until I'm confident that I likely have the best A class spawn in that ship's pool. My experience has shown me that after about 5-6 trade ups to the A class, I'm at the top of the A class spawns. This can still be a long camp but usually not as long as waiting for an S class spawn. Occasionally, I get lucky and an S class spawn comes along before I find that best A class. In those cases I call myself lucky and enjoy my new S class. If this doesn't happen, once I have the best A class, I end my camp and upgrade it to an S class knowing its base stats will be right on par with the best S class spawn.
In summary, there is a quicker path to a top tier S class ship by getting the best A class.
On a side note, on my current save I got lucky and got a really nice A class freighter on my second battle after I was first eligible for the free freighter. I did not realize how lucky until about a week later I got lucky again and got an S class freighter on the fifth reroll of the battle. When I compared my current A class to the S class the stats were almost the same. The tech and storage were the same.
Hope this helps give some a little better solution to the dreaded camps for S class ships.