Both are historical dramas set in the joseon era with fantasy elements (more so in moon sun than rebel). Both have the same vibe of sincere love, fight against corruption. But while The Moon that Embraces the Sun centers around the royals and nobles, rebel is more down to earth with story revolving around the normal folk aspiring to make a change. I love both dramas but feel Rebel has that something special that brings authenticity to it that I have yet to find in any other historical drama (that I've seen).
The stories themselves aren't that similar but I felt the vibe is. They are both cute dramas about high school students dealing with life and romance. Though romance is more central in Minami-kun no koibito: My Little Lover. Both also have light supernatural elements (time travel in Splash, shrinking in Minami-kun).
Both dramas deal with the psychological aspect of human nature as well as romance and life in general. MARS is a bit more deep and dark than It's okay, It's love but both are very good dramas. MARS is one of my absolute favorites, it's based on, and follows quite faithfully, the original manga by Fuyumi Soryo. I absolutely recommend you check it out! Like the phrase goes, it's an oldie but a goodie. ^_^