I'm pretty sure these things have existed in every version of ToA, and were actually 'introduced' in ToA. The most serious ones that Mac mentioned above, AI's not expanding, and some civ's not building social improvements (have been acknowledged as bugs by Stardock) mostly only happen on large and the largest of map sizes. These will not be noticed on smaller maps that much.
One way to 'correct' this behavior is to set all civ's to "Generic" personality setting (during game setup under opponents, i think). This makes all civ's expand much better, and also seems to make certain civs (such as Torians, which are notorious for not building any social improvements at all on a large % of their planets) build social improvements on all their planets... although I am still verifying this in my current game.