Elytra texture transparencies become opaque if any of the following are true:

• player is holding an item in the main or off hand
• player is wearing a pumpkin
• player is wearing a player head (Not affected by creeper, skeleton, wither skeleton, zombie, or dragon heads)
• player is Wearing an armor piece with an enchantment glow (If the elytra has an enchantment glow, it works properly)

Wearing the elytra without meeting any of the conditions listed above will render the texture as expected, with all transparencies working. I've included two comparison screenshots to demonstrate this, and the texture file used so you can test it for yourself. These textures were done via a resource pack.

I included a screenshot of the debug screen in case I missed anything in the environment. Yes, the screenshot is in 1.9-pre4, but I also just tested it in 1.9 (released as I'm typing this), and can confirm that the bug is still there.