All in all, I like the changes. The maneuverability categories work well for flying limitations. That's something I think some DMs forget about when running fliers. Once your category gets too low, it really limits what you can do in combat. If you have to waste one or two rounds to turn around and get back, you're seriously hurting in your economy of actions.
Looking at the templates, it seems the Bestial template comes at a fairly high cost. Other than that, the ones I'd be most likely to consider are Burrower, Hearty, Riding, or Flier. I don't know that the others are bad, but I'm not sure I'd get as much out of them.
That being said, I have two questions:
1) With the Riding template, do the two 1d4 attacks replace the standard 1d6 attack, or are they in addition to?
2) Is the only point of the War Trained ability (other than the +2 Str) to make it so you can wear armor? Not that it's a bad ability; I just wanted clarification.