There seem to be a lot of pictures of him where if there's a bright light shining in his eyes, his eyes kind of take on an amber glow. What you're seeing is a bright light shining in his eyes. It's not digitally altered because there are numerous photos of him with glowy amber eyes with light reflections.
Personally, I think that's a great shot of him. Very appealing.
One thing that I always notice with him is his open bite (his front teeth aren't aligned properly and have a space in front between his upper and lower teeth). It's kind of cute. I like it when actors have personality in their not-so-perfect teeth. His open bite also adds to his long-jawed appearance and the constant persing of his lips.
As for not being interested in watching him play a villain, IMO, he's a right bastard most of the time, but he definitely has his sympathetic side to him and you can't help but root for the guy sometimes. The morally gray characters (see: "gray"--most of the characters aren't all black or white--and Sylar's real last name being "Gray" is a big hint at that) are the most enjoyable (Sylar, Noah Bennet, Angela Petrelli, etc... being the most obviously morally ambiguous of the bunch).