It didn't start getting easy for me to backstab people until i got that Ninja roll perk
ehehe I found the ninja roll to be relatively worthless - just another stepping stone on the track to the Silent Running thing.
but to answer OP's question, I think it is mainly a problem (which I have had some of) of adjusting to the new interface in Skyrim. Sometimes it won't tell you the NPC's name when you're close enough to kill them, which is a pain, but the Sneak Critical will still work. As a general rule of thumb, if you're close enough for it to say "Pickpocket," then you're probably close enough to stab. You don't have to be 100% hidden, but it helps immensely, the chances go down quickly once that eye starts to open.
Or, if you're just having trouble being sneaky enough to get close without getting caught, remember to walk slowly when you're getting close, stick to the shadows (this is literally true, helps), and wear light armor or just clothes. Also, approaching from behind helps.