....Funny how these things always go...
Eh...I think it depends on the situation, like the art style, emotion, personality, etc.
Like, sometimes it fits when they've got large/medium eyes, other times it's better when they're smaller...
A good example is Junjou Romantica. There's an uke with big eyes, as he's pretty innocent ( wink ) and childish. There's also one with smaller eyes, as he's older, more serious, and more cynical. It just depends...yeah sweatdrop I dunno how to explain it.
...where and why, exactly, no one really knows...