Last time I (freeciv developer) were here, thread
http://forums.civfanatics.com/showthread.php?t=412202 was the result. To sum: Freeciv is more totally configurable than civ2, but that comes with the cost that simple modding is harder (things are not
simply something but one can configure what they are) SL at large seems to prefer simplicity over power and flexibility.
We can fix some minor problem here and there, but the big picture remains that freeciv devs and SL have incompatible philosophies to civ modding. It always amazes me to notice how the most minor things, byproducts, such as support for bigger number of nations, in freeciv are what you are interested about.
No hard feelings. The reason I'm checking here again today is that maybe we can achieve something together (between some individuals at least) even though larger movement to freeciv modding is rather unlikely.
If that "scenario must spread over many folders" is really the biggest problem, we've got it really easy
Flexibility and power of freeciv: Nothing forces you to setup scenario that way, it's just customary (for a reason, but still). Your mymod.serv and mymod.tilespec files should be in freeciv data directory root, but as they contain paths to everything else, you can otherwise setup your directory structure as you wish.
Also, I'd still be interested to get feedback about the freeciv modding tutorial draft I wrote for you. I'm presenting it to other audiences as well...
http://www.cazfi.net/freeciv/RulesetExample.txt
Oh, and self-promotion part: Today the Alien World ruleset I talked last time changed hands (well, I'm on both sides, but still). It's no longer mine alone, but now part of freeciv project. We're still not using graphics that would make any sense with the ruleset, but classic ruleset type gfx as fallback (See screenshot
http://www.cazfi.net/freeciv/alien/ )