Even with an updated SVN I regularly see AIs knocked out by barbarians. In a recent game, three AIs fell to barbarians, one couldnt expand beyond one city because of them, another lost their capital but were still able to expand a little, and the last was the Donviello. When half of the AIs are crippled or destroyed by barbarians, Id say thats a problem.
The barbarian system also makes initially placement too important. A civ that ends up on a peninsula has a huge advantage over other civs, far bigger than a civ with a similar placement in a vanilla or FFH2 game.
Then theres the killer stack of six highwaymen that shows up from time to time. Or the barbarian Aerons Chosen (which, thankfully, I havent seen since updating via SVN). Either one of those can wipe out multiple civs.
I wonder if playing on barbarian world would help this out at all. Im far more scared of lairs than I am of barbarian cities (which is counter-intuitive).