Unlike Preview, the Adobe Reader application allows you to change PDF highlight (comment) text colors via a standard Apple color chooser. Click Tools on the Reader Toolbar, and then Comment. The second button in the Comment Annotation section is highlight text, and defaults to canary yellow.
Highlight the document text, and then two-finger tap/control-right-click that highlighted text. On the contextual menu, you will see Properties…. The properties panel has a color well set to yellow. Click this color well, and a standard Apple color chooser will appear that allows you more creative control over your highlight color. When you click a color in the color chooser, it is not automatically updated in the color well, which remains dark grey. When you quit the color chooser, the selected color is updated in this color well and in your document. The next text that you select to highlight will receive a default yellow highlight.