Hi,
I think if the trees are both the same variety, the final form I.E. leaf size, internodes ect will be determined by it's growing location. Sun ,moisture, wind and the passing seasons will most likely make both trees look the same after a few years. They look different now because they probably grew in different locations. It's been my experience that immediate envoirnment is the biggest factor in determining what the older tree will look like. That being said , I really dislike grafts so I would select the most natural matching,transition and tapering of the trunk. If the graft is not too noticeable now it will tend to go away, if it is bulgy or uneven it may get more so as the trunk thickens. As far as height, the taller one will get a lot wider before it touches the ground resulting in a all around bigger tree. Again , where you're going to put it will be a big factor. Is it in a low spot, over a rock or a pond, on a rise. If it were me I would choose the shorter graft. If a grafted lower part buds back you have a different color and leaf tree growing below. Hope that helps
Steve

the one on the right looks feminine (dsc0157) - dsc01249
it wants to curve upward

the one on the left looks masculine (dsc0157) - dsc01248
it wants to spread and droop

I would keep the dsc01249 - the feminine
why?

-has a single potential leader that might/should be guided straight to a soft S shape. Initially it will look funny but the tree will balance it's shape next year. it's still young and flexible.
-the bark has characteristic, my kid would say "it looks like a snake"
-unless you're going to bonsai node length doesn't matter. node length can be controlled by holding back fertilizer or pinching off new growth.
-it has branches growing on the outside curves. This has been previously been properly stylized; branches usually grow in opposing pairs.

if you don't want it; tell me were you're going to return it...