I don't really agree with Blueblood as a bad guy. I agree hes not good, but he's really just an average stuck-up jerk, not like the rest of (most of) the villains here. Might I suggest make Nightmare Moon the Queen, and replace Blueblood with Chrysalis. Just an idea.
Actually, most of those are not really evil. Hydra - probably defending it's territory or hunting for food. Cockatrice - probably defending it's territory Trixie - was a show magician, those are expected to behave like that. Gilda - a Griffon. Those naturally eat Ponies, but she does not do it for her friend, which puts a lot of stress on her, mentally and physically ( note that she eats pony food despite being an obligate Carnivore, who will get ill from it ) Dragon - protecting it's territory and treasure, with the ponies attacking him and trying to steal it.