I haven't tried to read through this whole thread, but I have a couple thoughts on the issue of milking and scoring.
The reason I have no interest at all in milking games is that it requires absolutely insane nation management decisions. A well-run civilization would want as many improvements in each city as possible, but milkers have to deliberately limit their building of anything that produces culture if they want the game to last until 2050. Worse, since science improvements produce culture, milking strategies seem likely to seriously compromise a nation's science as well. Further, making cities productive rather than merely happy is almost completely irrelevant to the success of milking. Thus, milking is NOT about building up a great civilization, but rather is merely about manipulating the scoring rules.
If other people get their fun out of manipulating the scoring rules to the greatest possible advantage, that's fine. But for me, Civilization games are about building a great civilization, and that transcends the manipulations of a rules mechanic. I'll bend my play style a little to try to score a little higher, but I won't smash it to a million pieces.
I enjoy the GOTMs as a shared experience, and I do compete fairly seriously (and in one case so far, successfully) for "fastest finish" medals. Speeding up the finish as much as possible does require a little bit of "rules mechanic" manipulation, but it's mostly about building up a nation that is militarily and/or scientifically advanced as quickly as possible. I can live with that, and even when I don't win medals, coming close tells me I'm a good player whatever the score chart says.
Which brings me to the ultimate test of any scoring system: Can players who are simply trying to build great civilizations expect to score at least almost as well as players who deliberately manipulate the scoring system to their advantage? Unless a scoring system can achieve that kind of transparency, it will be at least as much a measure of players' willingness to go out of their way to manipulate the scoring system as it is of their true ability to build great civilizations. I hope those of you who are working on ideas for alternative scoring systems keep that in mind.
Another point: an analysis of any proposed scoring system must take into consideration how the scoring system itself will affect people's playing styles. Even if a scoring system makes 100% perfect sense for balancing past games, it might not make sense when players start adjusting their playing styles to the new scoring criteria. (And self-calibrating systems that look at relative statistics rather than absolute statistics are even more vulnerable to fluctuations in playing style.) That, too, is something that those who work on alternative scoring systems have to watch for.
I'd love to see a scoring system good enough that those of us who focus on the more abstract concept of building a successful civilization can get scores in the same ballpark as what rules mechanics get. But I'm not holding my breath.
One last thing: in my book, it should be next to impossible for a game that lasts until 2050 to be considered a true success. Any nation worth its salt should normally be able to achieve some sort of victory long before then, and choosing not to do so diminishes that nation. That's not to say that success should be measured solely or even primarily in terms of fastest finish, because a well-balanced nation will almost inevitably not reach any particular goal as quickly as it could if it compromised everything else in favor of that one goal. But rewarding nations for deliberately refusing to capture that last foreign city after all but conquering the world, or for refusing to claim the little bit of extra land needed for domination, or for deliberately destroying their own centers of culture in order to avoid cultural victory, represents a gross perversion of the game's underlying concept and a serious flaw in the scoring system. So my view, in a well-designed scoring system, winning fast should certainly not be the only consideration, but milking until 2050 should not be a viable option at all.
Nathan