You might as well just have them jump since the whole point of having two captains in the first place was to multi-task better; meaning they usually would be in two different regions of the area.
Requiring both captains to be present for vertical travel puts some limit on the ability. It means that only one captain can get up on a ledge by being thrown at a time, the other captain must find an alternate route, or wait below. It also means that the captain up on the ledge can't be thrown again, until they reunite with the other captain. Thus I think having the captains throw each other rather than simply be capable of jumping makes the ability more interesting and involve more strategy for how to use it.
Also, it means fewer buttons need to be assigned, which means the game isn't as complicated, which always strikes me as a good thing.
Regarding multi-tasking... I don't see how this idea really hampers it at all. This just means the captains have to be together briefly so one can throw the other and some pikmin up on a ledge. One captain can do "tasks" up on the ledge while the other can find "tasks" to do on the main ground. Thus "multitasking" is accomplished. Although I can imagine puzzles where you need captains on both sides of a gate at once would be cool...
Wait, what? How does throwing a Captain really detain from that and prevent the Pikmin from being the main focus?
It doesn't. Certainly this ability is less detrimental to the focus on the Pikmin than the punching upgrade for the captains or the sprays the captains could use on beasts.
My stylish, arcade-style game Egg Drop! is available to download to the iPhone, iPad, & iPod Touch http://itunes.apple.com/us/app/egg-drop/id443347380?mt=8