While I'm sure it's impossible to draw an exact ranking, I still think this exercice is interesting. I'll post my comments and thoughts.
I'm not sure why you don't count single traits. For example, I'm sure that everyone would have rated IND as the top trait in Vanilla/PTW and give it 1 point. You do it for AGR now, but maybe on the whole (since this is your wish) some traits are just better than others. Then you can add the combo synergy, etc...
I don't know why you give 1 point for multiplayer (MP ?). Your purpose is to rank the civs on the whole, so that must take MP into account within itself, not with an artificial point. A better way to do would be to see if any civ performs well in human hands AND in AI hands. For human, it would be to weigh if the civ on the whole is even better because of the human brain (I'm thinking of fast UUs eg.) ; for AI, it would be to weigh if it understands how to play this or that civ characteristic, or this or that general stuff which appears to be more important for the civ (SEA civs aren't played well because of suicide runs, etc...).
I think it would be better to clearly indicate that this ranking is for Emperor or above. As a Deity player, I now find it difficult to lack Alphabet at the beginning, not just because it's the most expensive initial tech, but because it leads to Writing and then very interesting and numerous techs. I think the point for Alphabet is deserved. We could even give it 2 points, and give 1 point to civs which can immediately research a non-initial tech (call that starting-tech synergy

).
While I understand and agree that MIL/SEA wastes part of the traits (cheap harbors), I don't know why EXP/SEA and EXP/MIL are antagonisms. EXP/SEA can play very well on a real continent map : first you get free towns, techs, contacts and no barbs from huts, and then you're the 1st to discover the other continent. I say tech lead there ! So there are maps where this combo is good. As for EXP/MIL, I don't understand the comment. I don't see why you can't build a few scouts to find your foes and get an early tech and city lead, and then build barracks and military. Surely the few missing warriors won't make that of a difference ? Of course on Deity the EXP trait is well wasted (see other stanza).
Another remark, in the opposite way : COM/SEA. I'm not sure if both gold bonuses end up in one bonus or not. I don't think so, but otherwise there would be an antagonism there.
Doc, why Spain and Arabia as top civs for 20k ?
Greece rated so high ? I think the system isn't perfect, though I'd like Greece to be the best civ of all.

I'm happy to see Byzantium so high, but I hope that the dromon not being a top UU has to do with the general scope of this ranking (includes pangea maps).
Why is Egypt rated so low ? In Vanilla/PTW it was clearly one of the top civs, because of its traits, the synergy between them, and a decent UU. Read Sullla's games, and he clearly states that Egypt is maybe the best civ all in all, and the AI played it well. But in C3C, IND was well toned down, and REL was a little toned too (anarchy). Add to that a war chariot which has to face ancient cavalries, better gallic swordsmen, etc... and AGR civs ! Egypt isn't a top civ anymore.
As for Maya, well I've never really played them, but we know IND isn't the top trait it used to be. They're AGR, which says they're a decent civ. But they have a very mediocre UU, let's face it. At least it could have been quite nice, but it was poorly implemented. Javelin throwers enslave units, are a decent early unit, even if a bit expensive. But the price isn't justified : enslaved units become slaves which don't have the IND tag. This means that the IND trait is wasted with them !! Mayans still have to build their workers, otherwise the IND trait is wasted. This is nonsense. And of course the Javelin upgrades to the crappy and poorly thought longbowman, which is a serious drawback. All in all, AGR/IND looked very promising (no doubt about that), but the civ representing this combo and C3C's flaws made it mediocre.