Well, since you're attempting to improve the feel of the system, individual lines running from the MC to each caliper is the way to do this. This creates individual activation of the calipers and is the preferred way to do it for performance reasons.
Running the calipers in series with each other (like the stock configuration) is fine, but the feel is diminished as one caliper has to start activating before the pressure can increase to the point of activating the other caliper. The reason it is done the way it is from the factory is for packaging reasons with the large rubber lines. Running two of those down from the MC would be difficult.
The newer bikes use a splitter block under the triple tree in an attempt to accomplish both goals, but it is still better to run individual lines from the MC to each caliper.
Running the calipers in series with each other (like the stock configuration) is fine, but the feel is diminished as one caliper has to start activating before the pressure can increase to the point of activating the other caliper. The reason it is done the way it is from the factory is for packaging reasons with the large rubber lines. Running two of those down from the MC would be difficult.
The newer bikes use a splitter block under the triple tree in an attempt to accomplish both goals, but it is still better to run individual lines from the MC to each caliper.