The true legacy of the Wachowskis, so close to pulling off the impossible that it is not wholly understandable in one viewing.
The central theme is the idea of karma. Actions affecting our lives, not just in this life but through several incarnations. Thrown in is the idea of connectedness, no one really being independent but connected and dependant on others.
The format through which these themes are worked are i believe 6 different times over three centuries. The same actors are used in their "same" roles in different time lines to give this understanding of "same" person ie reincarnation, the idea of a continuous soul.
While this same actor trick works, ie helps us in understanding the roles, the immutable characters, each story is cut up and interwoven with the others. Thus the film follows six stories unfolding in parallel, all working the same themes, following similar arches. As i said in the beginning, it is trying the almost impossible, and it is very difficult to follow in the first 2-3 sittings (i'm beyond ten). But i would really encourage you to put in the time, because in the end it does work and the film achieves it's objective of carrying ideas that are at the edge of what can be expressed in words (try explaining karma to anyone who hasn't heard about it, if you doubt)
In the end i think this is the true legacy of the Wachowskis. Matrix was off course fun, but to be honest the idea of living in a simulation world was just new, the delivery exiting, but eventually hot air. As an idea it really is not very solid and the Movie quite understandably does not work beyond the first, where "enlightenment" is achieved, and who can go beyond that in this mortal sphere.
The idea of karma on the other hand is as good a one as humans every had and tried to put into words. It is of the keys to human existence and here worked in a very watch-able package.