Because it happened like that historically, and didn't turn around until later in the war. If you look at the Japanese carrier strikes at Pearl, Ceylon, Midway or even Santa Cruz you will see they favored massing the individual carrier air wings into one giant hammer blow. The tactic was simple; overwhelm the opposition by weight of numbers. They were able to do this by grouping their carriers into one tight formation at the time of launch. This allowed the air wings to launch, assemble and attack as a group.
The Americans, on the other hand, operated in smaller TFs consisting of 1 or 2 carriers, but with coordination issues still to be worked out. Midway, in particular, was a good example of these problems with coordination. Despite having a clear-cut command structure, fairly good communications, and three carriers operating in close proximity, they nevertheless launched fragmented strikes. Some groups went in with no fighter cover, others never found the targets, etc.
"splendid was their tactic of diving upon our force from the direction of the sun, taking advantage of intermittent clouds"
-Captain Takahisa Amagai, KAGA, June 4th 1942