Of course there is the option of just making things harder.
Well, hacking thresholds are already pretty high, some of the highest in the game really, so a few more dice aren't going to shatter worlds.
One thing I've done in the past is to make it Logic or Program with the non-dominant skill taking a Teamwork position. Teamwork in this case meaning, you roll the dice for that attribute and add hits to the Dice Pool of the test. That makes it an average 1/3rd bonus from the lesser stat.
So, the Skiddie lets the Program run on alt preset standard and might be able to help adjust it with his meager Logic.
Meanwhile the ghetto-savant works his garbage-ass Program his way, using his sublime Logic. Sometimes the program surprisingly does what it was supposed to do without his urging, but mostly, he is throwing the code where it needs to be.
And, finally, the supreme virtuoso whips his homebrewed supertools into a stunning display of cyber-supremacy, with the perfect machinations of the Program taking the forefront, but being continuously guided and conducted by the virtuoso's god-like mental faculties.