Well I'd like to see some skills and attribute checks and some Radian AI improvements like it was fixed in Oblivion
Mind-Control Crime
http://www.tesnexus.com/downloads/file.php?id=24099
Used on anyone with legal rights, Charm, Command Humanoid, Demoralize, and Frenzy effects are now illegal. Victims can't tell if you're casting it on them (unless they have an Intelligence of 75+ or an Illusion skill of 50+), but other people nearby can. Witnesses will only be able to tell what you're doing if they have an Intelligence of 50 or higher, an Illusion skill of 25 or higher, or training as a Guard. Like with other crimes, how they react to it depends on the witness in question. Often, though, they'll call the Guards. If you mind control a Guard, and a witnessing civilian raises the alarm, the guard will believe them and try to arrest you (Assuming they're not in your thrall or completely insane). If you're seen mind-controlling a victim, any crimes they commit while under a Frenzy or Command Humanoid effect will be counted towards your bounty as well. Theoretically, they wouldn't be responsible for their actions at this time, but I've never seen such a crime end in any other way than the Frenzied victim being killed. If the victim dies while under a Frenzy or Command Humanoid effect, you will be treated as the murderer.
Stealthy Absorbs and Drains v1
http://www.tesnexus.com/downloads/file.php?id=28292
This mod makes Absorb and Drain Attribute and Skill spells non-hostile if your skill in the corresponding
school AND your sneak skill are both higher than the casting cost of the spell. This makes it possible to do
things like absorb a merchant's mercantile skill to get better deals when buying equipment or a passing NPC's
luck to get better odds at the arena without alerting anyone and causing them to go on the offensive.
This is a small mod intended to add a little bit of variety and usefulness to some otherwise pretty useless
spells, and to make quests in the city a little more interesting for stealth-type characters who use magic.
Put it in its Place - Enhanced Grabbing
http://www.tesnexus.com/downloads/file.php?id=19847
Better detection and reaction of NPC on havok movement with dragging and telekineses, really great improvement over Oblivion system.
Duke Patricks - Near Miss Magic And Arrows Alert The Target
http://www.tesnexus.com/downloads/file.php?id=16150
Make NPC aware about shooting arrows and casting spells around them, so no more casting fireball or shooting over head of NPC without of any reaction from their AI
About invisible runes, I'd like return of Detect Enchanting spell so NPC thats have such spell can see such runes on ground as well as player can see them, if magnitude of spell and skills was high enough, another thing thats such spell can handle its highlighting plaques and inscription on the walls with magical aura (certain puzzles can be based on it), detect dropped enchanted items on ground (no more pixel hunting for small ring, or disarmed weapon in high grass, as well can be used for detecting missed throwing weapons and arrows)