Because being able to transport armies (especially large ones) over the sea is a privilege that has to be earned. It's expensive (you seen the cost of raised ships?) and to achieve that ability you have to be a large kingdom/empire with a decent bit of coastline.
Rome 2 allows anybody and everybody to just sail their armies in to the sea at no extra cost. So does Attila. What happens? We get absolutely ridiculous scenarios like landlocked barbarian tribes, who live landlocked north of Hungary, who have no knowledge of boats or sailing, whose ancestors have no knowledge of boats or sailing, who would see a sailing boat and think it was some kind of giant container for storing grain, or perhaps for bathing in, and would need to be TOLD it's for sailing in water...
And those tribes just march to the coast, climb in to magic boats that instantly materialize out of thin air, cost no time or money to make, and are sailed expertly by men who inexplicably have no knowledge of sailing, and they sail all over the world raiding and looting at will.
And it's fu***** ridiculous, mate.
However I do agree that playing as the Byzantines (for example) is tedious when you have to constantly raise army, raise boats, click army, click embark, then click where the ships need to assemble, then when they're all assembled click army, merge army, click boats, merge boats, click merged army, embark on merged boats, then send them to their destination. It's really really tedious. It gets worse when you raise an army of 301 men but the province you raised them in only had 3 boats and you can't possibly squeeze that 1 man in the boats, so that means none of the men get to go on a boat and you have to bring in a navy from another province to get them on the boats.
We don't need to remove ships entirely to fix this however, just add a button that automatically raises both army and ships from a province and puts the army on the ships.