Well we just did something unorthodox and as you say not everyone was pleased. Problem with these kinds of things is that they get discovered and not exposed. They can not be addressed unless they are exposed, so it's our duty to expose these things. In the long run the game is better for it. Many times no one wants to listen cause they might have to take some sort of action.
The scoring system is one thing that Firaxis has not addressed. People have exposed many exploits in this game that firaxis has fixed with patches, etc. (bombard anywhere, trading cities, 'multi'-cheat, etc.). I don't know if Firaxis ever reads the GOTM threads, so someone will have to post something in the general discussions forum to alert them to this. I do know they at least read the general discussion forums.
Like Cartouche Bee said, someone could have found this exploit and continued doing this, without anyone discovering it. They could use this, then abandon the city on the last turn. Unless someone downloaded the game and watched the replay no one would know. You would be puzzled "why the heck did they abandon a city on the very last turn?" Now we know.
Realm beyond Epics sounds like a good tournament, but like you said, it's not for everyone. The goal of GOTM is just using the standard rules of the game going after the standard victory conditions. If you award points for certain things, people will find ways to use these to be able to rack up the 'score' more or easier than someone who played just as good of a game and was of the same skill level. With enough people you will always find more efficient/easier ways of racking up the points.
The tournament on this site is emphasizing fast finishes. They don't want to totally ignore points (someone who finished 1 turn later, but scored 1000 more points should not lose). They've gone to the extreme of weighting turns to score with a 10:1 ratio (the game score accounts for 9% of your tournament score). But even with this method someone who finished real early with a one-city challange will most likely lose to someone who finished much later with a bigger empire. The guy with the 1 city played a better game IMO.
What I kinda meant by 'any better ideas', I was asking for changes that should by done to the scoring system that Firaxis could do to make it more reasonable. For example:1. Award an early win bonus based on turns, not years, and it being high enough that could never be achieved through 'milking'. 2. Award points for wonders, improvements, great leaders, etc.