This is not a mainstream movie. You may be very distracted by the presence of jokey 20th century anachronisms in this otherwise grave movie about the artistic genius, Caravaggio. 17th century merchants use hand-held calculators, modern instruments play at the parties, local scribes use typewriters, servants dress in modern dinner jackets. I sure don't know what it all means. I guess you can impute many meanings to it.
You may also be irritated by the director in his insistence that everyone is motivated by homoerotic impulses. This facet of the presentation is really more about Derek Jarman than Caravaggio.
Well, I'm not sure that the movie has much to say about Caravaggio at all. After all, Caravaggio shocked his era with his revisionist hagiography - saints with peasant faces, torn clothes and dirty fingernails - probably realistic but iconoclastic in its time, and contrary to a century of previous tradition. Moreover, Caravaggio almost invented the modern system of a consistently represented light source, showing the actual impact of light on his subjects. These key points are barely touched by the script.
But I think you probably should just let those irritations wash over you, and accept the movie for what it is. It uses the style and mood of his paintings to reflect his life, and it incorporates that precise aesthetic into the movie's own visuals. The movie looks like what Caravaggio's own moving pictures might have looked like if he could have created them in 1600.
Is it a good movie? Who knows? It's not so well remembered after a decade or so, but it exhibits a memorable gift for creating and sustaining a mood, and for breathing life into Caravaggio's canvases. It also speculates about the everyday life that must have circulated around the creation of those masterpieces.
I was willing to forgive a lot of artistic pretension and rhetorical dialogue for the superb visuals and atmosphere, and I took vivid memories away from the film. You may feel the same way.