Taking the Kayenta Trail to both the Middle and Upper pools, the trip only took me about an hour. I went in the late afternoon a little after 4, and the trail was heavily packed with people. Since the trail is easy/moderate, there were a lot of families with their children. The path was mostly wide and there were no chains or narrow paths to navigate.
I went after hiking Observation Point, and added this as a quick bonus before I ended the day. That being said, going even later, maybe around 5, or early in the morning probably would have been the best time of day to avoid crowds. Still, it was a pretty hike!
If the Lower pools are open when you go, I would suggest taking the Lower Pools up, and the Kayenta Trail down! That way you get to see each trail all in one. Had the trail been open, this definitely would have been my route of choice.