Ze_PilOt has posted very interesting numbers here: viewtopic.php?p=54477#p54477
One should be careful when interpreting these numbers however. If a faction has a high win ratio, that does not necessarily say much about the strength of that faction. To see why lets assume for the sake of example that you're a 1600 rating player and you play UEF, and you currently have a win ratio of 52%. Now UEF gets a big buff. What happens? You win more games so for a short time your win ratio goes higher than 52%. But then trueskill quickly recognizes this and your rating increases, which means you play against better players. The result is that your win ratio goes back to around 50%. Even though UEF was buffed, its overall win ratio may increase only very little! The effect is not in the win ratio, the effect is simply that UEF players increase some number of points in rating. In other words, if a faction has a win ratio of 60%, that may actually mean that that faction is massively OP.
So to measure whether a faction is strong vs another faction, a different method is needed. One way to do this is to use trueskill itself. We add 4 "pseudo-players" to the player base: "UEF", "Aeon", "Seraphim", "Cybran". Now every 1v1 game we count as a 2v2 game. If Voodoo plays UEF vs Zock as Cybran, we count that as a 2v2 game with {Voodoo, UEF} as team 1 and {Zock, Cybran} as team 2. If we then compute the trueskill of all players using this method, we can see how many rating points each faction is worth. For instance if UEF gets a rating of 1200 and Cybran gets a rating of 1300, that means that Cybran is a stronger faction worth 100 rating points. Playing Cybran at the skill of a 1900 player makes you just as strong as playing UEF at the skill of a 2000 player. Hopefully this explanation is clear.
(note all numbers in this post are just an example)