Acid3 is a great test and helped implementors align on features everyone agrees on are useful, such as Media Queries, Selectors, CSS Fonts, and the latest of CSS Colors. Having said that, there are some minor issues. In order to reach a hundred tests quite a few obscure details of the DOM are tested as well as two controversial features.
One of the goals we have with developing the new DOM standard is simplifying constructs. E.g. the previous DOM specification had a number of restrictions on DocumentType nodes which we removed. However, test 98 of Acid3 tests document.doctype.ownerDocument. Acid3 is also specific on the exceptions it tests which conflicts with the recent plan of changing the exception model for the web. The plan is to move exceptions towards reusing DOMException. Acid3 tests RangeException which conflicts with that goal.
The details of the DOM are still somewhat in flux and implementors are interested in changing for the better. Whether to keep SVG Animation (something tested by Acid3) is still being debated by the SVG and CSS WGs. As we are flexible with changing standards for the better these days, lets be flexible with changing their tests too.