I find that when pleating to a very large Sett that it is sometimes helpful to "cheat" the Sett slightly which results in alternating pleat depths like you describe. You just need to insure that no Pleat Depth is too shallow and destroys the Swish.

Another alternative is to pleat so that the reveal on the outside of the Kilt shows alternating elements of the Tartan.

For example: Let's say you have a hypothetical Tartan that includes alternating Red Stripes, and Yellow stripes. But the distance of the Total Sett from one Red Stripe to the next Red Stripe is 12 inches. But the distance of 1/2 of the Sett or between a Red Stripe and a Yellow Stripe is 6".
You could choose to pleat the Kilt with alternating one Red Striped pleat, & one Yellow Striped Pleat.
A Kilt like in my example would look similar to some Military Kilts done in the Stewart Hunting Tartan. We Pleat it with alternating Red And Yellow Stripes and call it "The Catsup & Mustard Kilt".