This is in mplayer2, but not in mplayer. Can the feature either be backported from mplayer2, or can WiiMC be based on mplayer2, so it can work?

Ordered chapters are an official mkv feature which lets a mkv file specify a separate chapter. For instance, you may have several episodes of a series with the same opening; the opening can be encoded a single time in a single .mkv and playing any file that uses it will include the opening.