Very much like the idea of colour coding; it would make differentiating easier for the less fluff-endowed species and just make things tidier (no more 'M/F' and variations thereof in the names), but it seems there should be a button to opt out or some form 'neutral' option. And limiting character customization based on gender would bug me, seeing as I tend to make fairly androgynous-looking characters that seem to confuse people (one more reason to really like the colour coded names XD).
Oh, and as for new manes, bring 'em on! Bring them in buckets! Grow out ALL the floof!