Extreme inaccuracies.
Almost all the units are off. Pharaoh's bowmen? Flaming pigs? Roman ninjas? The portrayal of "non-civilized" factions as barbarians without clothing or armor? Axes are expensive weapons? Everyone who isn't part of a faction is a rebel slave? Ships are an afterthought, and the buildings are totally unrealistic. As if building a temple in some random city would all of a sudden give your troops superpowers!
The diplomacy is nonexistent, and the AI (both in the strategy and battle maps) is so stupid that it is almost impossible to lose a battle. Harder difficulty settings do not make the AI smarter. They make it hate you more (so it will not ceasefire even if you are sieging their last settlement with 3 full stacks), skew auto-resolve in its favor, and give combat units retarded attack and defense bonuses (peasants killing Spartans). And did I mention that hoplites in this game fight in the Macedonian manner? WTF?
So basically this is the antithesis of games like EU, HOI, or Victoria in terms of AI capabilities and realism. This game is very fun, but you can conquer the whole map within 100 years fairly easily. Another thing - because conquest is so easy and there is no diplomacy, the movement rate is artificially limited by default (it can be modified) - distances that in reality could be crossed in a couple of months take years to traverse. Basically play this game for the very fun battles, feeling of conquest, and the excellent mods.
The mods are what really make this game great. Hyperrealistic mods like EB and others like Invasio Barbarorum, XGM, RTR, and Roma Surrectum are what you should try after finishing the Imperial Campaign in RTW. Get the expansions, but don't bother with playing vanilla campaigns. Mods are the way to go.