First off, to familiarize myself with the system and give examples, approximate ratings for official factions. Bear in mine these numbers are not %s and the average baseline is set to 40, not 50. And of course for different maps/situations different factions are stronger or weaker (fungus for natives, tech feeding for yang or domai, trading for morgan, high sea for pirates, etc). Here we go:

Rush: 50 (+ for worms to fight and get pods, - for morale drop)
Build: 35 (+ for effic and early formers, - for no +1 eng/square)
Average: 42.5

Rush: 46 (+ for free perims and indust, - for poor research/energy)
Build: 46 (+ for free Planned/PS, + for +1 growth/Indust, - for bad energy/research and no demo)
Average: 46

Rush: 32 (- for -1 Support, + for starting with armour)
Build: 58 (+ for easy +1 eng/square and commerce, - for no Planned so hard pop booms)
Average: 45

Rush: 40 (nothing to see here)
Build: 45 (+ for talent, votes, and bigger bases)
Average: 42.5

Rush: 56 (+ for Morale and speeders, - for indust)
Build: 35 (+ for wormcash, - for Indust and no wealth)
Average: 45.5

Rush: 58 (+ for worms)
Build: 28 (- for no +1 eng/square, - for indust penalty, + for wormcash and pods)
Average: 43

Rush: 45 (+ for tech)
Build: 53 (+ for effic+research, - for hard pop booms)
Average: 49

Rush: 45 (+ for early/good probes)
Build: 42 (+ for sharetech)
Average: 43.5

Rush: 35 (- for no tech to rush with, + for troops)
Build: 55 (+ for facilis/SPs, - for terrible research)
Average: 45

Rush: 60 (+ for massive support and fanatic)
Build: 30 (- for research)
Average: 45

Rush: 44 (+ for quick impact, - for probe issues)
Build: 55 (+ for research, - for drone problems)
Average: 49.5

Rush: n/a (sea start)
Build: 47? (+ for uncontested expansion on sea, - for growth/effic)
Average: 47?

Rush: 62 (+ for Morale, offence, battle ogre, tech start)
Build: 48 (+ for growth, rec tanks, directed research, - for no demo)
Average: 55

Rush: 57 (+ for planet, defence, and battle ogre)
Build: 53 (+ for rec tanks, directed research, defence)
Average: 55
Comments on these ratings should not be the focus of posts, they are primarily examples. If you think I have made a major error (got a faction's stat off by more than 5-8) then let me know with reasoning, but I don't want to get bogged down by tweaking the examples by a few points when these ratings for official factions are not going to be used anywhere in the near future.
Now, let's have some suggestions on which custom factions are good to start with. Probably best to start with 10 or so that have some interesting gameplay and philosophy, then review.
http://alphacentauri2.info/wiki/Category:Custom_factions is a list of on wiki custom factions.
I'd like to have some of the factions in development, if you faction makers want to pick your favourites that'd be good. Mostly looking for factions which add something new and distinct to the game.
My initial interested list:
http://alphacentauri2.info/wiki/Crimson_Comrades - getting a lot of use, strong philosophy and playstyle
AntiMind - mostly to test the rating system, also seems popular. Alternatively:
http://alphacentauri2.info/wiki/The_Rangers_of_ChironOne of the many terraformer factions.
http://alphacentauri2.info/wiki/The_Freelancers - Free HQ is cool and interesting. But need a balanced version, because +3 Econ is insane.
http://alphacentauri2.info/wiki/Guardians_of_Morality