Perhaps Stealth should be altered to include a mastery perk of "cleaning up the scene of the crime" or something. Under a certain level maybe you leave a hair or some of your blood or a boot print behind and a Battlemage Investigator can come and use Mysticism to figure out your identity..but after a certain level of Stealth you become smarter and figure out how to remove evidence from the crime scene. At level 100 you are uncatchable, with no witnesses.
I haven't played the Thief series, but there was a neat mod for TESIV by scruggs... what was it called? It added arrows that could 'turn off' light sources, and ropes you could climb, and all sorts of fun things to manipulate the environment in favor of stealth. Part of it also including the importance of concealed/hiding dead/unconscious NPCs.
There's something I would like to see (maybe) from what little I managed to play of Gothic. In the game, at the point where you would "kill" an NPC (or be killed by an NPC), they instead will be prone on the ground, helpless, for about half a minute. You can then decided if you want to deliver a "finishing blow" to kill the NPC, or if you just wanted them disabled but not killed. I think this might be a cool thing to implement in a TES game: it would enable the ability to mug NPCs, or subdue them. I can see it being used in quests where you need to rough up or beat some sense into an NPC before they will talk to you. Maybe after beating an NPC, you can let them go (if they promise not to attack you again), or you could try to force them to serve you or be your pack mule (and they might revolt and attack you rather than be enslaved), or escort you to hidden loot, or get info out of them. So, in other words, there's a lot of opportunity for role playing and having different reactions and things to say to a 'beaten' NPC, rather than just slaughter half the non-law-abiding population.