I believe that riot-skirmisher combos would indeed usually be countered by pure skirmisher forces, or by reliable artillery kiting, since you'd then overpower the enemy's skirmishers through sheer numbers (assuming equal mass), or at the very least, trade even with them. Once the enemy's skirmishers are gone, you could then safely kite the riots to death.
However, if the enemy is using mostly skirmishers in their skirmisher-riot combo, then it'd probably be better to focus heavily on raiders and/or fast assaults (like the Ravager or Halberd), since chances are that the enemy riot would be overwhelmed by so many fast units barreling down towards it (and the skirmishers).
Alternatively, you could try to sneak up to the skirmisher-riot combo with cloaked riot and/or assault units (such as Reavers and/or Knights hidden by an Iris), and not only overpower the riots through sheer numbers, but also negate the skirmishers' range advantage over the riots.