Frankly, at this point, given that CCP and Falcon have basically been making the Federation out (event-wise) to be The Best At Everything, I don't really know why we need to worry about the negative points of the other factions.
I mean, if the Minmatar take on the Fed, they get stomped. If an Amarr Holder takes on the Fed? Stomped. Operation Highlander? The Caldari get stomped, even if the only way to guarantee it is CCP re-spawning waves of dreadnoughts. If the Fed loses the militia war? No problem, they win anyway via a great new president, news articles, and screwing over suddenly stupid Caldari megas. Oh, wait, the Fed militia just took all systems? Well, they win again, because they exercised a scorched-earth policy when withdrawing.
Hell, in the Dust arena, the Caldari players beat the Gallente. Didn't matter. CCP rewrote it so that the Gallente won the battle of Caldari Prime on the ground as well, completely (EvE Source).
At this point, trying to find dark spots for the Caldari seems pointless. Why bother? We have one faction that is True and Good, and beats everyone else via plot armor. , so forget nuance. We have a space opera now. Might as well conform.