Webgl speed is not so good with this, since it has to copy the texture to vram every time it changes (internal issue).
Different size circles is trivial, but for different color circles you mainly have these options:
1. Use this plugin to draw the circles using any color. You'd be only drawing to this so if you clear it to transparent you can have anything underneath show just fine.
2. A second option could be to use the paster object which is similar to the canvas object, but was made with webgl in mind. It doesn't draw circles but it does allow making any color. So you could do some clever things with blend modes, a circle sprite, and the paste action.
3. You could use a white circle sprite with the tint effect. This by far would be the simplest.
4. As a last resort you could just use a lot of animation frames with different colors.