This was one of my favorite Enterprise episodes. Personally, I have no problem with it being a stand alone Twilight Zone Star Trek episode. Not everything needs to spring into an extended story arc. The mystery behind the station itself is part of what makes it good, the viewer can let their imagination run wild.
And that's what I did in my books -- I let my imagination run wild and extrapolated a possible explanation. The only difference is that I get to share what I imagined with other people. The books aren't canonical, just might-have-beens. So my speculative explanation doesn't preclude fanfic authors or just fans from imagining different explanations.
And no, it didn't "need" to be an extended story arc, but I needed material that I could
get extended story arcs from, because I'm being paid to come up with them. And that particular episode suggested possibilities that I could do interesting things with.
That being said, it could be that the station interacts differently with each species it encounters. Some races would consider trading a crew member in exchange for vital, life saving repairs a fair deal. In those cases the station may very well list a crew member as a payment option, or insist that was the only way it would render help. The idea of building a biologically based neural net would certainly appeal to some species. They may even rationalize that the exchanged person wouldn't truly be dead, they would live on as a component of a greater whole (the Binars from TNG might have looked at it that way). With more sentimental creatures like humans, deception was obviously the strategy it employed in getting what it wanted/needed.
One of the major elements of my Ware storyline, in fact, was exploring how different civilizations reacted differently to the cost in lives. The system itself wasn't as intelligently adaptive as you suggest, but various races were more or less willing to adapt to its demands, or to find their own different ways of coping with those demands.
I doubt every ship loses a crew member - not every creature would necessarily be compatible.
Of course not -- that would be too much of a giveaway. If every ship that patronized such a station suffered a "fatality," the pattern would soon become obvious and people would stop coming to them. And they'd only take new captives when they needed to replace one of the old ones.
For example, I don't know if the station could've successfully integrated a Tholian into it's system. It looked like it used primarily humanoids when they showed the processing chamber.
I took that as a production error, essentially. Remember: When
Enterprise first arrived, the conditions on the station were extremely far from Minshara-class -- a liquid helium atmosphere near absolute zero. Nothing humanoid could survive that. The stations were meant to adapt to the needs of all kinds of life forms, so it was a poor design/directorial decision to show only humanoids in the primary data core.
Indeed, I went to town with this in
Live by the Code -- the benefit that the Ware could provide by allowing species physically incapable of inventing their own technology to gain the means to travel in space and interact with each other, versus the cost that the technology exacts from its users. Is it a price worth paying? I found that a fascinating ethical question to explore.
As for future Enterprises, after Archer filed his report with Starfleet all active crews would be aware of the danger posed by this station. I would think Galaxy class starships would be too large for even that station to accommodate anyway. Also, in the 23rd and 24th centuries Starbases would be far more common than they were in Archer's time. Starfleet would also have a lot more ships to render assistance, so something like the Enterprise D needing the station would be much less likely.
It's unlikely the technology would've been encountered much after the ENT era, since after all it had replicator tech that was well beyond what the Federation had until the 24th century.