Ever since season 2 finale and the focus on the color of the "Wolfen eye" (LOL), a lot of chitter-chatter had been in circulation. Obvious choice was, the fans associating colors with the state of a Wolfenkind -
Red - Alphas
Gold - Betas
Blue - Omegas.
But then Mr. Jeff denied such and said it would be studied upon in S03. With Scott eyes turning red for few seconds, we are again on the topic. So hear me out,
I think the color has to do with the emotion and power of a Wolfkin
An alpha has to keep other betas in line and has to be focused and has to have high adrenaline. Rage Power... perhaps it manifests in red color. Downside - You're real angry! Clarity of mind and decisions are questionable - e.g Old Peter, Derek and New Alphas!
A beta on the other hand only has to follow. Normal state of werewolf sanity. Ooo shiny gold! :P
Scott lost his alpha when Peter died, he's alive now but no longer is an alpha. If blue eyes truly meant an omega, Scott would've shown it ever since S01. It wasn't so, he had a purpose and teen life to live. He is now becoming a leader... red-shift anyone?
Blue eyes in my present belief hold the place of emotional clarity and peace of mind. Jackson was revived a wolfenkind at an peaceful/regret-free state of mind, hence the blue tints.
PS: If you look carefully, Peter though not shown ever once in wolf-form manifested blue eyes when he probed Isaac's mind for the whereabouts of Boyd and Erica. He could be in peace now or has a carefree attitude.
Blue are the eyes of Undead/revived wolves!
Maybe it means nothing at all! Any thoughts?