I love both colours, but most folks tend to pick red which means it's smart to keep a brown dragon. If your pet is a different colour to everyone else's, you never ever lose it on a screen. This is really useful in an event or group hunt. Or if you have multiple pets. If you tamed different coloured pets so you could tell them apart, you don't want the EC making them identical
I really just want pets to be the same colour and look as good in EC as they do in the CC. Some of the graphics just don't seem to match the personality you imagine that creature to have, or the graphics just don't look as "finished". Kitsune being an obvious example... they look like spoiled lap dogs. I'm not a huge fan of the CC graphic, but at least it looked cheeky, like a creature that would giggle.
Wenchy