I really watch it this way:
Matrix
Matrix Reloaded (starting at the basketball court/skip everything before)
Matrix Revolution
I actually liked Revolution for some odd reason. I mean all three are at their core 'good' movies. Matrix being the best of them, obviously, but despite what a lot of people seem to think about the birth of the sequels, I think they tie together nicely. There's a bunch of great documentries that come with the ultimate collection that go over a lot of the process and story, and I think that helped me appreciate Revolutions.
I mean I like LOTR and all, but there are far more boring parts to those movies than the Matrix Trilogy, which is why 9 times out of 10 id rather watch the Matrix Trilogy.