I've used unlabelled, coloured weakAuras bars for years now and my method for choosing colours has always been to try to as close as possible match the dominant colour of the ability's icon. That way you can use colours that are similar-ish and have it remain fairly intuitive (you'll notice Blizzard does try to have icons for each class have varied ish colours, a concept other MMO interface designers seem to miss. Look at the icons in Forge f.e.)
Another helpful thing to do is have the group be a normal static group, not a dynamic one. That way the each bar is always in exactly the same place, and "reading" them is a little bit faster/easier (which afaik is a definite cognition/interface principle: "where it is is what it is"). I know sometimes that leads to gaps between the bars, but more often than not you'll have most of the bars always up anyways (for rotational things anyways).