I use YUI compression, because, at least on my servers, it is about twice as fast, compressed files are slightly smaller, and unlike with the PHP alternatives, properly written CSS5 always still validates and properly written JS code always still runs without errors. I have a strong general dislike for Java, but in this particular application, YUI compression has worked significantly better for me than the PHP code.
I am not posting this to argue with your decision to remove it from future versions. I use a forked customized version of Autoptimize to meet unique needs and can leave it in my private version. I am merely wondering whether YUI compression is going to be removed due to Java security-vulnerably concerns, because it isn't being widely used by plugin users, because you have found an operational problem, or for some other reason.