For those that care, going with one posters constant example of 4 Agility against Medium range, and assuming 2 ranks in the appropriate skill, the 2D results for the check (2 ability, 2 proficiency, 3 difficulty) results in the highest point at 2 successes, 0 advantage (this is Net after cancelling with failures and threat). That makes up 251,226 of 4,718,592 possible results, or about 5% of the results. Expanding the selection outward so that successes range from 1 to 3, advantages range from -1 to 1 (-1 means a net Threat) now encompasses 37% of the results. A second expansion gets successes ranging from 0 to 4 and advantages range from -2 to 2 now encompasses nearly 70% of the possible outcomes. The possible results that allow for a second or greater hit (2 or more Net Advantage) is only 10.5% of the possible results with the most likely result being 1 success and 2 advantage. Removing one Difficulty die would reduce the Net negative results (obviously) and would move the results slightly more down and to the right (so 1 more Net Advantage).
Ahh, the joy of having an app that takes in the dice counts and spits out a nice table of charts. What is interesting is how sharp the spike is of the 2D surface showing that the big results (high successes or high advantages, but never both) are really the minor results of all the dice.