Any recommendations for small to medium plants that add fall color, especially flowers?

In Michigan, for fall flowers you might be limited to perennial chrysanthemums and the like. Check your local nurseries. Don't buy the chrysanthemums at the big box stores that have been forced to bloom out of season. They won't survive the winter. To get the "real thing" your real nurseries are the place.

Other plants like heucheras have a huge range of different foliage, and some change to beautiful leaf colors in the fall, though. Nice, small plants that are also perennial, and have pretty flowers in the spring as well.

Specially bred asters (bred for smallness); there's also some goldenrods bred for small stature and garden adaptability. Chrysanthemums also, though if planted this late probably will not survive the winter.

Others to consider are Turtleheads and Sedum.

Toad lilies are great too if you have shade or part shade. Also my English Daisies often rebloom in the fall

Yes, autumn joy sedum is great for fall color. Some black-eyed susans will keep blooming for me into early fall if kept deadheaded. In addition, you may want to look into reblooming irises. Dwarf, intermediate, and border bearded irises may meet your height requirements. Although not perennials, cosmos from seed usually blooms nicely in the fall for me and can reseed itself. I literally just throw seeds on the ground in the spring and keep the area watered.

Clara Curtis daisies are nice, too. They spread like weeds for me. Tree-mail me,Schuler, and I can send you some for postage.