I've used dd to successfully clone USB sticks, but when the written data is a small percentage of the device's capacity, I was wondering if there's a smarter way of doing it.

What I'm talking about is scenarios when the stick has several partitions, that together stretch to fill 25% of the available capacity. The dd utility works well, but takes a long time to write a previously created image. Of course, I could create the partitions manually, and then use dd to clone each partition, one at a time, but that would be too cumbersome.

Do you guys know a simpler method?

Take a look at partimage (it should be available for installation in most linux systems). As stated in the official page:
Maybe this is what you're looking for.

I see partimage does so on a partition level. My case has several partitions. I could use it just as dd, but would have to do so multiple times, once for each partition.

You could try clonezilla which can do partitions and or drives.

http://clonezilla.org/