Create Multisport Challenges
Challenges are presently cycling or running, exclusively. However, for participants who mix cycling and running (and maybe swimming) the result is distributed mediocrity. That run which displaces a ride hurts the ride rankings, and vice-versa.
I recommend a multi-sport challenge. For example, on a distance basis, use a conversion factor for run miles to cycling miles. For example using Ironman distances, running miles would be equivalent to 4.27 cycling miles, and swimming miles would be equivalent to 46.7 cycling miles.
For vertical gain, swimming obviously doesn't really apply, but for running versus cycling, either the same conversion factor could be used, or it could be recognized steeper routes are possible with running, and a smaller conversion could apply, or even no conversion (1=1).
An alternate challenge type would be one which actively promoted balancing running and cycling distance. For example, the following formula could be used:
S = sqrt[ C × R ]
where C is cycling distance, R is running distance, and "sqrt" specifies square root. With this approach, if you have a choice between a run or a ride, the one which increases your net distance by the maximal percentage is the optimal one for your score. If you do the same distance runs every time, and the same distance rides every time, then you maximize the score by having the same number of runs and rides. An alternative scheme could be used to give preference to a given fraction (other than 50%) for runs versus rides, but I don't see much point to that:
S = C^f × R^(1-f)
where ^ is exponentiation, f is the power to which the argument is raised, and C and R are as before. Here f is the optimal fraction of cycling activities of the same length assuming running activities also of the same length and a fixed number of total activities (f = 0.5 gives the balanced formula above, f = 1 gives a cycling challenge, f = 0 gives a running challenge).
In any case, you get my idea...