This is a cool sounding game idea by the way!
Personally I'd go with several species. I feel it'd be more interesting for the player to look at and easier to create an emotional connection for each dragon because each one would look quite unique . Plus on some other level it may create an even greater feeling of all dragons banding together to survive! ha ha .
Well the dragons are sitll one species, the game wouldn't' work the way we want otherwise, another issue is why dragons would have all these differences, if there's no reason, that lends more to high fantasy then to the low fantasy type game I'm going for.